| Previous changeset 3:7950e4c52972 (2017-06-23) Next changeset 5:b7652b7c97bd (2017-10-20) |
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Commit message:
Uploaded |
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added:
Hammock/dist/Hammock.jar Hammock/matrices/blosum100.txt Hammock/matrices/blosum30.txt Hammock/matrices/blosum35.txt Hammock/matrices/blosum40.txt Hammock/matrices/blosum45.txt Hammock/matrices/blosum50.txt Hammock/matrices/blosum55.txt Hammock/matrices/blosum60.txt Hammock/matrices/blosum62.txt Hammock/matrices/blosum62.txt~ Hammock/matrices/blosum65.txt Hammock/matrices/blosum70.txt Hammock/matrices/blosum75.txt Hammock/matrices/blosum80.txt Hammock/matrices/blosum85.txt Hammock/matrices/blosum90.txt Hammock/matrices/gonnet250.txt Hammock/matrices/mcla71.txt Hammock/matrices/pam250.txt Hammock/settings/misc/blosum62.freq_rownorm Hammock/settings/settings.prop Hammock/settings/settings.prop~ hammock.xml test-data/input.fa test-data/output_clusters.csv test-data/output_sequences.csv tool_dependencies.xml wrapper.sh |
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removed:
v.1.1.0/Hammock/dist/Hammock.jar v.1.1.0/Hammock/matrices/blosum100.txt v.1.1.0/Hammock/matrices/blosum30.txt v.1.1.0/Hammock/matrices/blosum35.txt v.1.1.0/Hammock/matrices/blosum40.txt v.1.1.0/Hammock/matrices/blosum45.txt v.1.1.0/Hammock/matrices/blosum50.txt v.1.1.0/Hammock/matrices/blosum55.txt v.1.1.0/Hammock/matrices/blosum60.txt v.1.1.0/Hammock/matrices/blosum62.txt v.1.1.0/Hammock/matrices/blosum62.txt~ v.1.1.0/Hammock/matrices/blosum65.txt v.1.1.0/Hammock/matrices/blosum70.txt v.1.1.0/Hammock/matrices/blosum75.txt v.1.1.0/Hammock/matrices/blosum80.txt v.1.1.0/Hammock/matrices/blosum85.txt v.1.1.0/Hammock/matrices/blosum90.txt v.1.1.0/Hammock/matrices/gonnet250.txt v.1.1.0/Hammock/matrices/mcla71.txt v.1.1.0/Hammock/matrices/pam250.txt v.1.1.0/Hammock/settings/misc/blosum62.freq_rownorm v.1.1.0/Hammock/settings/settings.prop v.1.1.0/Hammock/settings/settings.prop~ v.1.1.0/hammock.xml v.1.1.0/test-data/input.fa v.1.1.0/test-data/output_clusters.csv v.1.1.0/test-data/output_sequences.csv v.1.1.0/tool_dependencies.xml v.1.1.0/wrapper.sh |
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| diff -r 7950e4c52972 -r 22b245c1bb94 Hammock/dist/Hammock.jar |
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| Binary file Hammock/dist/Hammock.jar has changed |
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| diff -r 7950e4c52972 -r 22b245c1bb94 Hammock/matrices/blosum100.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/Hammock/matrices/blosum100.txt Fri Jun 23 06:33:16 2017 -0400 |
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| @@ -0,0 +1,31 @@ +# Matrix made by matblas from blosum100_3.iij +# * column uses minimum score +# BLOSUM Clustered Scoring Matrix in 1/3 Bit Units +# Blocks Database = /data/blocks_5.0/blocks.dat +# Cluster Percentage: >= 100 +# Entropy = 1.4516, Expected = -1.0948 + A R N D C Q E G H I L K M F P S T W Y V B Z X * +A 8 -3 -4 -5 -2 -2 -3 -1 -4 -4 -4 -2 -3 -5 -2 1 -1 -6 -5 -2 -4 -2 -2 -10 +R -3 10 -2 -5 -8 0 -2 -6 -1 -7 -6 3 -4 -6 -5 -3 -3 -7 -5 -6 -4 -1 -3 -10 +N -4 -2 11 1 -5 -1 -2 -2 0 -7 -7 -1 -5 -7 -5 0 -1 -8 -5 -7 5 -2 -3 -10 +D -5 -5 1 10 -8 -2 2 -4 -3 -8 -8 -3 -8 -8 -5 -2 -4 -10 -7 -8 6 0 -4 -10 +C -2 -8 -5 -8 14 -7 -9 -7 -8 -3 -5 -8 -4 -4 -8 -3 -3 -7 -6 -3 -7 -8 -5 -10 +Q -2 0 -1 -2 -7 11 2 -5 1 -6 -5 2 -2 -6 -4 -2 -3 -5 -4 -5 -2 5 -2 -10 +E -3 -2 -2 2 -9 2 10 -6 -2 -7 -7 0 -5 -8 -4 -2 -3 -8 -7 -5 0 7 -3 -10 +G -1 -6 -2 -4 -7 -5 -6 9 -6 -9 -8 -5 -7 -8 -6 -2 -5 -7 -8 -8 -3 -5 -4 -10 +H -4 -1 0 -3 -8 1 -2 -6 13 -7 -6 -3 -5 -4 -5 -3 -4 -5 1 -7 -2 -1 -4 -10 +I -4 -7 -7 -8 -3 -6 -7 -9 -7 8 2 -6 1 -2 -7 -5 -3 -6 -4 4 -8 -7 -3 -10 +L -4 -6 -7 -8 -5 -5 -7 -8 -6 2 8 -6 3 0 -7 -6 -4 -5 -4 0 -8 -6 -3 -10 +K -2 3 -1 -3 -8 2 0 -5 -3 -6 -6 10 -4 -6 -3 -2 -3 -8 -5 -5 -2 0 -3 -10 +M -3 -4 -5 -8 -4 -2 -5 -7 -5 1 3 -4 12 -1 -5 -4 -2 -4 -5 0 -7 -4 -3 -10 +F -5 -6 -7 -8 -4 -6 -8 -8 -4 -2 0 -6 -1 11 -7 -5 -5 0 4 -3 -7 -7 -4 -10 +P -2 -5 -5 -5 -8 -4 -4 -6 -5 -7 -7 -3 -5 -7 12 -3 -4 -8 -7 -6 -5 -4 -4 -10 +S 1 -3 0 -2 -3 -2 -2 -2 -3 -5 -6 -2 -4 -5 -3 9 2 -7 -5 -4 -1 -2 -2 -10 +T -1 -3 -1 -4 -3 -3 -3 -5 -4 -3 -4 -3 -2 -5 -4 2 9 -7 -5 -1 -2 -3 -2 -10 +W -6 -7 -8 -10 -7 -5 -8 -7 -5 -6 -5 -8 -4 0 -8 -7 -7 17 2 -5 -9 -7 -6 -10 +Y -5 -5 -5 -7 -6 -4 -7 -8 1 -4 -4 -5 -5 4 -7 -5 -5 2 12 -5 -6 -6 -4 -10 +V -2 -6 -7 -8 -3 -5 -5 -8 -7 4 0 -5 0 -3 -6 -4 -1 -5 -5 8 -7 -5 -3 -10 +B -4 -4 5 6 -7 -2 0 -3 -2 -8 -8 -2 -7 -7 -5 -1 -2 -9 -6 -7 6 0 -4 -10 +Z -2 -1 -2 0 -8 5 7 -5 -1 -7 -6 0 -4 -7 -4 -2 -3 -7 -6 -5 0 6 -2 -10 +X -2 -3 -3 -4 -5 -2 -3 -4 -4 -3 -3 -3 -3 -4 -4 -2 -2 -6 -4 -3 -4 -2 -3 -10 +* -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 1 |
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| diff -r 7950e4c52972 -r 22b245c1bb94 Hammock/matrices/blosum30.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/Hammock/matrices/blosum30.txt Fri Jun 23 06:33:16 2017 -0400 |
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| @@ -0,0 +1,31 @@ +# Matrix made by matblas from blosum30.iij +# * column uses minimum score +# BLOSUM Clustered Scoring Matrix in 1/5 Bit Units +# Blocks Database = /data/blocks_5.0/blocks.dat +# Cluster Percentage: >= 30 +# Entropy = 0.1424, Expected = -0.1074 + A R N D C Q E G H I L K M F P S T W Y V B Z X * +A 4 -1 0 0 -3 1 0 0 -2 0 -1 0 1 -2 -1 1 1 -5 -4 1 0 0 0 -7 +R -1 8 -2 -1 -2 3 -1 -2 -1 -3 -2 1 0 -1 -1 -1 -3 0 0 -1 -2 0 -1 -7 +N 0 -2 8 1 -1 -1 -1 0 -1 0 -2 0 0 -1 -3 0 1 -7 -4 -2 4 -1 0 -7 +D 0 -1 1 9 -3 -1 1 -1 -2 -4 -1 0 -3 -5 -1 0 -1 -4 -1 -2 5 0 -1 -7 +C -3 -2 -1 -3 17 -2 1 -4 -5 -2 0 -3 -2 -3 -3 -2 -2 -2 -6 -2 -2 0 -2 -7 +Q 1 3 -1 -1 -2 8 2 -2 0 -2 -2 0 -1 -3 0 -1 0 -1 -1 -3 -1 4 0 -7 +E 0 -1 -1 1 1 2 6 -2 0 -3 -1 2 -1 -4 1 0 -2 -1 -2 -3 0 5 -1 -7 +G 0 -2 0 -1 -4 -2 -2 8 -3 -1 -2 -1 -2 -3 -1 0 -2 1 -3 -3 0 -2 -1 -7 +H -2 -1 -1 -2 -5 0 0 -3 14 -2 -1 -2 2 -3 1 -1 -2 -5 0 -3 -2 0 -1 -7 +I 0 -3 0 -4 -2 -2 -3 -1 -2 6 2 -2 1 0 -3 -1 0 -3 -1 4 -2 -3 0 -7 +L -1 -2 -2 -1 0 -2 -1 -2 -1 2 4 -2 2 2 -3 -2 0 -2 3 1 -1 -1 0 -7 +K 0 1 0 0 -3 0 2 -1 -2 -2 -2 4 2 -1 1 0 -1 -2 -1 -2 0 1 0 -7 +M 1 0 0 -3 -2 -1 -1 -2 2 1 2 2 6 -2 -4 -2 0 -3 -1 0 -2 -1 0 -7 +F -2 -1 -1 -5 -3 -3 -4 -3 -3 0 2 -1 -2 10 -4 -1 -2 1 3 1 -3 -4 -1 -7 +P -1 -1 -3 -1 -3 0 1 -1 1 -3 -3 1 -4 -4 11 -1 0 -3 -2 -4 -2 0 -1 -7 +S 1 -1 0 0 -2 -1 0 0 -1 -1 -2 0 -2 -1 -1 4 2 -3 -2 -1 0 -1 0 -7 +T 1 -3 1 -1 -2 0 -2 -2 -2 0 0 -1 0 -2 0 2 5 -5 -1 1 0 -1 0 -7 +W -5 0 -7 -4 -2 -1 -1 1 -5 -3 -2 -2 -3 1 -3 -3 -5 20 5 -3 -5 -1 -2 -7 +Y -4 0 -4 -1 -6 -1 -2 -3 0 -1 3 -1 -1 3 -2 -2 -1 5 9 1 -3 -2 -1 -7 +V 1 -1 -2 -2 -2 -3 -3 -3 -3 4 1 -2 0 1 -4 -1 1 -3 1 5 -2 -3 0 -7 +B 0 -2 4 5 -2 -1 0 0 -2 -2 -1 0 -2 -3 -2 0 0 -5 -3 -2 5 0 -1 -7 +Z 0 0 -1 0 0 4 5 -2 0 -3 -1 1 -1 -4 0 -1 -1 -1 -2 -3 0 4 0 -7 +X 0 -1 0 -1 -2 0 -1 -1 -1 0 0 0 0 -1 -1 0 0 -2 -1 0 -1 0 -1 -7 +* -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 1 |
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| diff -r 7950e4c52972 -r 22b245c1bb94 Hammock/matrices/blosum35.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/Hammock/matrices/blosum35.txt Fri Jun 23 06:33:16 2017 -0400 |
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| @@ -0,0 +1,31 @@ +# Matrix made by matblas from blosum35.iij +# * column uses minimum score +# BLOSUM Clustered Scoring Matrix in 1/4 Bit Units +# Blocks Database = /data/blocks_5.0/blocks.dat +# Cluster Percentage: >= 35 +# Entropy = 0.2111, Expected = -0.1550 + A R N D C Q E G H I L K M F P S T W Y V B Z X * +A 5 -1 -1 -1 -2 0 -1 0 -2 -1 -2 0 0 -2 -2 1 0 -2 -1 0 -1 -1 0 -5 +R -1 8 -1 -1 -3 2 -1 -2 -1 -3 -2 2 0 -1 -2 -1 -2 0 0 -1 -1 0 -1 -5 +N -1 -1 7 1 -1 1 -1 1 1 -1 -2 0 -1 -1 -2 0 0 -2 -2 -2 4 0 0 -5 +D -1 -1 1 8 -3 -1 2 -2 0 -3 -2 -1 -3 -3 -1 -1 -1 -3 -2 -2 5 1 -1 -5 +C -2 -3 -1 -3 15 -3 -1 -3 -4 -4 -2 -2 -4 -4 -4 -3 -1 -5 -5 -2 -2 -2 -2 -5 +Q 0 2 1 -1 -3 7 2 -2 -1 -2 -2 0 -1 -4 0 0 0 -1 0 -3 0 4 -1 -5 +E -1 -1 -1 2 -1 2 6 -2 -1 -3 -1 1 -2 -3 0 0 -1 -1 -1 -2 0 5 -1 -5 +G 0 -2 1 -2 -3 -2 -2 7 -2 -3 -3 -1 -1 -3 -2 1 -2 -1 -2 -3 0 -2 -1 -5 +H -2 -1 1 0 -4 -1 -1 -2 12 -3 -2 -2 1 -3 -1 -1 -2 -4 0 -4 0 -1 -1 -5 +I -1 -3 -1 -3 -4 -2 -3 -3 -3 5 2 -2 1 1 -1 -2 -1 -1 0 4 -2 -3 0 -5 +L -2 -2 -2 -2 -2 -2 -1 -3 -2 2 5 -2 3 2 -3 -2 0 0 0 2 -2 -2 0 -5 +K 0 2 0 -1 -2 0 1 -1 -2 -2 -2 5 0 -1 0 0 0 0 -1 -2 0 1 0 -5 +M 0 0 -1 -3 -4 -1 -2 -1 1 1 3 0 6 0 -3 -1 0 1 0 1 -2 -2 0 -5 +F -2 -1 -1 -3 -4 -4 -3 -3 -3 1 2 -1 0 8 -4 -1 -1 1 3 1 -2 -3 -1 -5 +P -2 -2 -2 -1 -4 0 0 -2 -1 -1 -3 0 -3 -4 10 -2 0 -4 -3 -3 -1 0 -1 -5 +S 1 -1 0 -1 -3 0 0 1 -1 -2 -2 0 -1 -1 -2 4 2 -2 -1 -1 0 0 0 -5 +T 0 -2 0 -1 -1 0 -1 -2 -2 -1 0 0 0 -1 0 2 5 -2 -2 1 -1 -1 0 -5 +W -2 0 -2 -3 -5 -1 -1 -1 -4 -1 0 0 1 1 -4 -2 -2 16 3 -2 -3 -1 -1 -5 +Y -1 0 -2 -2 -5 0 -1 -2 0 0 0 -1 0 3 -3 -1 -2 3 8 0 -2 -1 -1 -5 +V 0 -1 -2 -2 -2 -3 -2 -3 -4 4 2 -2 1 1 -3 -1 1 -2 0 5 -2 -2 0 -5 +B -1 -1 4 5 -2 0 0 0 0 -2 -2 0 -2 -2 -1 0 -1 -3 -2 -2 5 0 -1 -5 +Z -1 0 0 1 -2 4 5 -2 -1 -3 -2 1 -2 -3 0 0 -1 -1 -1 -2 0 4 0 -5 +X 0 -1 0 -1 -2 -1 -1 -1 -1 0 0 0 0 -1 -1 0 0 -1 -1 0 -1 0 -1 -5 +* -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 1 |
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| diff -r 7950e4c52972 -r 22b245c1bb94 Hammock/matrices/blosum40.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/Hammock/matrices/blosum40.txt Fri Jun 23 06:33:16 2017 -0400 |
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| @@ -0,0 +1,31 @@ +# Matrix made by matblas from blosum40.iij +# * column uses minimum score +# BLOSUM Clustered Scoring Matrix in 1/4 Bit Units +# Blocks Database = /data/blocks_5.0/blocks.dat +# Cluster Percentage: >= 40 +# Entropy = 0.2851, Expected = -0.2090 + A R N D C Q E G H I L K M F P S T W Y V B Z X * +A 5 -2 -1 -1 -2 0 -1 1 -2 -1 -2 -1 -1 -3 -2 1 0 -3 -2 0 -1 -1 0 -6 +R -2 9 0 -1 -3 2 -1 -3 0 -3 -2 3 -1 -2 -3 -1 -2 -2 -1 -2 -1 0 -1 -6 +N -1 0 8 2 -2 1 -1 0 1 -2 -3 0 -2 -3 -2 1 0 -4 -2 -3 4 0 -1 -6 +D -1 -1 2 9 -2 -1 2 -2 0 -4 -3 0 -3 -4 -2 0 -1 -5 -3 -3 6 1 -1 -6 +C -2 -3 -2 -2 16 -4 -2 -3 -4 -4 -2 -3 -3 -2 -5 -1 -1 -6 -4 -2 -2 -3 -2 -6 +Q 0 2 1 -1 -4 8 2 -2 0 -3 -2 1 -1 -4 -2 1 -1 -1 -1 -3 0 4 -1 -6 +E -1 -1 -1 2 -2 2 7 -3 0 -4 -2 1 -2 -3 0 0 -1 -2 -2 -3 1 5 -1 -6 +G 1 -3 0 -2 -3 -2 -3 8 -2 -4 -4 -2 -2 -3 -1 0 -2 -2 -3 -4 -1 -2 -1 -6 +H -2 0 1 0 -4 0 0 -2 13 -3 -2 -1 1 -2 -2 -1 -2 -5 2 -4 0 0 -1 -6 +I -1 -3 -2 -4 -4 -3 -4 -4 -3 6 2 -3 1 1 -2 -2 -1 -3 0 4 -3 -4 -1 -6 +L -2 -2 -3 -3 -2 -2 -2 -4 -2 2 6 -2 3 2 -4 -3 -1 -1 0 2 -3 -2 -1 -6 +K -1 3 0 0 -3 1 1 -2 -1 -3 -2 6 -1 -3 -1 0 0 -2 -1 -2 0 1 -1 -6 +M -1 -1 -2 -3 -3 -1 -2 -2 1 1 3 -1 7 0 -2 -2 -1 -2 1 1 -3 -2 0 -6 +F -3 -2 -3 -4 -2 -4 -3 -3 -2 1 2 -3 0 9 -4 -2 -1 1 4 0 -3 -4 -1 -6 +P -2 -3 -2 -2 -5 -2 0 -1 -2 -2 -4 -1 -2 -4 11 -1 0 -4 -3 -3 -2 -1 -2 -6 +S 1 -1 1 0 -1 1 0 0 -1 -2 -3 0 -2 -2 -1 5 2 -5 -2 -1 0 0 0 -6 +T 0 -2 0 -1 -1 -1 -1 -2 -2 -1 -1 0 -1 -1 0 2 6 -4 -1 1 0 -1 0 -6 +W -3 -2 -4 -5 -6 -1 -2 -2 -5 -3 -1 -2 -2 1 -4 -5 -4 19 3 -3 -4 -2 -2 -6 +Y -2 -1 -2 -3 -4 -1 -2 -3 2 0 0 -1 1 4 -3 -2 -1 3 9 -1 -3 -2 -1 -6 +V 0 -2 -3 -3 -2 -3 -3 -4 -4 4 2 -2 1 0 -3 -1 1 -3 -1 5 -3 -3 -1 -6 +B -1 -1 4 6 -2 0 1 -1 0 -3 -3 0 -3 -3 -2 0 0 -4 -3 -3 5 2 -1 -6 +Z -1 0 0 1 -3 4 5 -2 0 -4 -2 1 -2 -4 -1 0 -1 -2 -2 -3 2 5 -1 -6 +X 0 -1 -1 -1 -2 -1 -1 -1 -1 -1 -1 -1 0 -1 -2 0 0 -2 -1 -1 -1 -1 -1 -6 +* -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 1 |
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| diff -r 7950e4c52972 -r 22b245c1bb94 Hammock/matrices/blosum45.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/Hammock/matrices/blosum45.txt Fri Jun 23 06:33:16 2017 -0400 |
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| @@ -0,0 +1,31 @@ +# Matrix made by matblas from blosum45.iij +# * column uses minimum score +# BLOSUM Clustered Scoring Matrix in 1/3 Bit Units +# Blocks Database = /data/blocks_5.0/blocks.dat +# Cluster Percentage: >= 45 +# Entropy = 0.3795, Expected = -0.2789 + A R N D C Q E G H I L K M F P S T W Y V B Z X * +A 5 -2 -1 -2 -1 -1 -1 0 -2 -1 -1 -1 -1 -2 -1 1 0 -2 -2 0 -1 -1 0 -5 +R -2 7 0 -1 -3 1 0 -2 0 -3 -2 3 -1 -2 -2 -1 -1 -2 -1 -2 -1 0 -1 -5 +N -1 0 6 2 -2 0 0 0 1 -2 -3 0 -2 -2 -2 1 0 -4 -2 -3 4 0 -1 -5 +D -2 -1 2 7 -3 0 2 -1 0 -4 -3 0 -3 -4 -1 0 -1 -4 -2 -3 5 1 -1 -5 +C -1 -3 -2 -3 12 -3 -3 -3 -3 -3 -2 -3 -2 -2 -4 -1 -1 -5 -3 -1 -2 -3 -2 -5 +Q -1 1 0 0 -3 6 2 -2 1 -2 -2 1 0 -4 -1 0 -1 -2 -1 -3 0 4 -1 -5 +E -1 0 0 2 -3 2 6 -2 0 -3 -2 1 -2 -3 0 0 -1 -3 -2 -3 1 4 -1 -5 +G 0 -2 0 -1 -3 -2 -2 7 -2 -4 -3 -2 -2 -3 -2 0 -2 -2 -3 -3 -1 -2 -1 -5 +H -2 0 1 0 -3 1 0 -2 10 -3 -2 -1 0 -2 -2 -1 -2 -3 2 -3 0 0 -1 -5 +I -1 -3 -2 -4 -3 -2 -3 -4 -3 5 2 -3 2 0 -2 -2 -1 -2 0 3 -3 -3 -1 -5 +L -1 -2 -3 -3 -2 -2 -2 -3 -2 2 5 -3 2 1 -3 -3 -1 -2 0 1 -3 -2 -1 -5 +K -1 3 0 0 -3 1 1 -2 -1 -3 -3 5 -1 -3 -1 -1 -1 -2 -1 -2 0 1 -1 -5 +M -1 -1 -2 -3 -2 0 -2 -2 0 2 2 -1 6 0 -2 -2 -1 -2 0 1 -2 -1 -1 -5 +F -2 -2 -2 -4 -2 -4 -3 -3 -2 0 1 -3 0 8 -3 -2 -1 1 3 0 -3 -3 -1 -5 +P -1 -2 -2 -1 -4 -1 0 -2 -2 -2 -3 -1 -2 -3 9 -1 -1 -3 -3 -3 -2 -1 -1 -5 +S 1 -1 1 0 -1 0 0 0 -1 -2 -3 -1 -2 -2 -1 4 2 -4 -2 -1 0 0 0 -5 +T 0 -1 0 -1 -1 -1 -1 -2 -2 -1 -1 -1 -1 -1 -1 2 5 -3 -1 0 0 -1 0 -5 +W -2 -2 -4 -4 -5 -2 -3 -2 -3 -2 -2 -2 -2 1 -3 -4 -3 15 3 -3 -4 -2 -2 -5 +Y -2 -1 -2 -2 -3 -1 -2 -3 2 0 0 -1 0 3 -3 -2 -1 3 8 -1 -2 -2 -1 -5 +V 0 -2 -3 -3 -1 -3 -3 -3 -3 3 1 -2 1 0 -3 -1 0 -3 -1 5 -3 -3 -1 -5 +B -1 -1 4 5 -2 0 1 -1 0 -3 -3 0 -2 -3 -2 0 0 -4 -2 -3 4 2 -1 -5 +Z -1 0 0 1 -3 4 4 -2 0 -3 -2 1 -1 -3 -1 0 -1 -2 -2 -3 2 4 -1 -5 +X 0 -1 -1 -1 -2 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 0 0 -2 -1 -1 -1 -1 -1 -5 +* -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 1 |
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| diff -r 7950e4c52972 -r 22b245c1bb94 Hammock/matrices/blosum50.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/Hammock/matrices/blosum50.txt Fri Jun 23 06:33:16 2017 -0400 |
| b |
| @@ -0,0 +1,31 @@ +# Matrix made by matblas from blosum50.iij +# * column uses minimum score +# BLOSUM Clustered Scoring Matrix in 1/3 Bit Units +# Blocks Database = /data/blocks_5.0/blocks.dat +# Cluster Percentage: >= 50 +# Entropy = 0.4808, Expected = -0.3573 + A R N D C Q E G H I L K M F P S T W Y V B Z X * +A 5 -2 -1 -2 -1 -1 -1 0 -2 -1 -2 -1 -1 -3 -1 1 0 -3 -2 0 -2 -1 -1 -5 +R -2 7 -1 -2 -4 1 0 -3 0 -4 -3 3 -2 -3 -3 -1 -1 -3 -1 -3 -1 0 -1 -5 +N -1 -1 7 2 -2 0 0 0 1 -3 -4 0 -2 -4 -2 1 0 -4 -2 -3 4 0 -1 -5 +D -2 -2 2 8 -4 0 2 -1 -1 -4 -4 -1 -4 -5 -1 0 -1 -5 -3 -4 5 1 -1 -5 +C -1 -4 -2 -4 13 -3 -3 -3 -3 -2 -2 -3 -2 -2 -4 -1 -1 -5 -3 -1 -3 -3 -2 -5 +Q -1 1 0 0 -3 7 2 -2 1 -3 -2 2 0 -4 -1 0 -1 -1 -1 -3 0 4 -1 -5 +E -1 0 0 2 -3 2 6 -3 0 -4 -3 1 -2 -3 -1 -1 -1 -3 -2 -3 1 5 -1 -5 +G 0 -3 0 -1 -3 -2 -3 8 -2 -4 -4 -2 -3 -4 -2 0 -2 -3 -3 -4 -1 -2 -2 -5 +H -2 0 1 -1 -3 1 0 -2 10 -4 -3 0 -1 -1 -2 -1 -2 -3 2 -4 0 0 -1 -5 +I -1 -4 -3 -4 -2 -3 -4 -4 -4 5 2 -3 2 0 -3 -3 -1 -3 -1 4 -4 -3 -1 -5 +L -2 -3 -4 -4 -2 -2 -3 -4 -3 2 5 -3 3 1 -4 -3 -1 -2 -1 1 -4 -3 -1 -5 +K -1 3 0 -1 -3 2 1 -2 0 -3 -3 6 -2 -4 -1 0 -1 -3 -2 -3 0 1 -1 -5 +M -1 -2 -2 -4 -2 0 -2 -3 -1 2 3 -2 7 0 -3 -2 -1 -1 0 1 -3 -1 -1 -5 +F -3 -3 -4 -5 -2 -4 -3 -4 -1 0 1 -4 0 8 -4 -3 -2 1 4 -1 -4 -4 -2 -5 +P -1 -3 -2 -1 -4 -1 -1 -2 -2 -3 -4 -1 -3 -4 10 -1 -1 -4 -3 -3 -2 -1 -2 -5 +S 1 -1 1 0 -1 0 -1 0 -1 -3 -3 0 -2 -3 -1 5 2 -4 -2 -2 0 0 -1 -5 +T 0 -1 0 -1 -1 -1 -1 -2 -2 -1 -1 -1 -1 -2 -1 2 5 -3 -2 0 0 -1 0 -5 +W -3 -3 -4 -5 -5 -1 -3 -3 -3 -3 -2 -3 -1 1 -4 -4 -3 15 2 -3 -5 -2 -3 -5 +Y -2 -1 -2 -3 -3 -1 -2 -3 2 -1 -1 -2 0 4 -3 -2 -2 2 8 -1 -3 -2 -1 -5 +V 0 -3 -3 -4 -1 -3 -3 -4 -4 4 1 -3 1 -1 -3 -2 0 -3 -1 5 -4 -3 -1 -5 +B -2 -1 4 5 -3 0 1 -1 0 -4 -4 0 -3 -4 -2 0 0 -5 -3 -4 5 2 -1 -5 +Z -1 0 0 1 -3 4 5 -2 0 -3 -3 1 -1 -4 -1 0 -1 -2 -2 -3 2 5 -1 -5 +X -1 -1 -1 -1 -2 -1 -1 -2 -1 -1 -1 -1 -1 -2 -2 -1 0 -3 -1 -1 -1 -1 -1 -5 +* -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 1 |
| b |
| diff -r 7950e4c52972 -r 22b245c1bb94 Hammock/matrices/blosum55.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/Hammock/matrices/blosum55.txt Fri Jun 23 06:33:16 2017 -0400 |
| b |
| @@ -0,0 +1,31 @@ +# Matrix made by matblas from blosum55.iij +# * column uses minimum score +# BLOSUM Clustered Scoring Matrix in 1/3 Bit Units +# Blocks Database = /data/blocks_5.0/blocks.dat +# Cluster Percentage: >= 55 +# Entropy = 0.5637, Expected = -0.4179 + A R N D C Q E G H I L K M F P S T W Y V B Z X * +A 5 -2 -2 -2 0 -1 -1 0 -2 -2 -2 -1 -1 -3 -1 2 0 -4 -2 0 -2 -1 -1 -5 +R -2 8 -1 -2 -4 1 0 -3 0 -4 -3 3 -2 -3 -3 -1 -1 -3 -2 -3 -1 0 -1 -5 +N -2 -1 8 2 -3 0 0 0 1 -4 -4 0 -3 -4 -2 1 0 -5 -2 -4 4 0 -1 -5 +D -2 -2 2 8 -4 0 2 -2 -1 -4 -5 -1 -4 -5 -2 0 -1 -5 -3 -4 5 1 -2 -5 +C 0 -4 -3 -4 13 -4 -4 -3 -4 -2 -2 -4 -2 -3 -3 -1 -1 -4 -3 -1 -4 -4 -2 -5 +Q -1 1 0 0 -4 7 2 -2 1 -4 -3 2 0 -4 -1 0 -1 -2 -1 -3 0 4 -1 -5 +E -1 0 0 2 -4 2 7 -3 -1 -4 -4 1 -3 -4 -1 0 -1 -3 -2 -3 1 5 -1 -5 +G 0 -3 0 -2 -3 -2 -3 8 -2 -5 -5 -2 -3 -4 -3 0 -2 -3 -4 -4 -1 -3 -2 -5 +H -2 0 1 -1 -4 1 -1 -2 11 -4 -3 0 -2 -1 -3 -1 -2 -3 2 -4 0 0 -1 -5 +I -2 -4 -4 -4 -2 -4 -4 -5 -4 6 2 -4 2 0 -3 -3 -1 -3 -1 4 -4 -4 -1 -5 +L -2 -3 -4 -5 -2 -3 -4 -5 -3 2 6 -3 3 1 -4 -3 -2 -3 -1 1 -4 -3 -1 -5 +K -1 3 0 -1 -4 2 1 -2 0 -4 -3 6 -2 -4 -1 0 -1 -4 -2 -3 0 1 -1 -5 +M -1 -2 -3 -4 -2 0 -3 -3 -2 2 3 -2 8 0 -3 -2 -1 -2 -1 1 -3 -2 -1 -5 +F -3 -3 -4 -5 -3 -4 -4 -4 -1 0 1 -4 0 9 -5 -3 -3 2 4 -1 -5 -4 -2 -5 +P -1 -3 -2 -2 -3 -1 -1 -3 -3 -3 -4 -1 -3 -5 10 -1 -1 -5 -4 -3 -2 -1 -2 -5 +S 2 -1 1 0 -1 0 0 0 -1 -3 -3 0 -2 -3 -1 5 2 -4 -2 -2 0 0 -1 -5 +T 0 -1 0 -1 -1 -1 -1 -2 -2 -1 -2 -1 -1 -3 -1 2 6 -3 -2 0 -1 -1 -1 -5 +W -4 -3 -5 -5 -4 -2 -3 -3 -3 -3 -3 -4 -2 2 -5 -4 -3 15 3 -4 -5 -3 -3 -5 +Y -2 -2 -2 -3 -3 -1 -2 -4 2 -1 -1 -2 -1 4 -4 -2 -2 3 9 -2 -3 -2 -1 -5 +V 0 -3 -4 -4 -1 -3 -3 -4 -4 4 1 -3 1 -1 -3 -2 0 -4 -2 5 -4 -3 -1 -5 +B -2 -1 4 5 -4 0 1 -1 0 -4 -4 0 -3 -5 -2 0 -1 -5 -3 -4 5 2 -1 -5 +Z -1 0 0 1 -4 4 5 -3 0 -4 -3 1 -2 -4 -1 0 -1 -3 -2 -3 2 5 -1 -5 +X -1 -1 -1 -2 -2 -1 -1 -2 -1 -1 -1 -1 -1 -2 -2 -1 -1 -3 -1 -1 -1 -1 -1 -5 +* -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 1 |
| b |
| diff -r 7950e4c52972 -r 22b245c1bb94 Hammock/matrices/blosum60.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/Hammock/matrices/blosum60.txt Fri Jun 23 06:33:16 2017 -0400 |
| b |
| @@ -0,0 +1,31 @@ +# Matrix made by matblas from blosum60.iij +# * column uses minimum score +# BLOSUM Clustered Scoring Matrix in 1/2 Bit Units +# Blocks Database = /data/blocks_5.0/blocks.dat +# Cluster Percentage: >= 60 +# Entropy = 0.6603, Expected = -0.4917 + A R N D C Q E G H I L K M F P S T W Y V B Z X * +A 4 -1 -1 -2 0 -1 -1 0 -2 -1 -1 -1 -1 -2 -1 1 0 -3 -2 0 -2 -1 0 -4 +R -1 5 0 -1 -3 1 0 -2 0 -3 -2 2 -1 -3 -2 -1 -1 -3 -2 -2 -1 0 -1 -4 +N -1 0 6 1 -2 0 0 0 1 -3 -3 0 -2 -3 -2 1 0 -4 -2 -3 3 0 -1 -4 +D -2 -1 1 6 -3 0 2 -1 -1 -3 -3 -1 -3 -3 -1 0 -1 -4 -3 -3 4 1 -1 -4 +C 0 -3 -2 -3 9 -3 -3 -2 -3 -1 -1 -3 -1 -2 -3 -1 -1 -2 -2 -1 -3 -3 -2 -4 +Q -1 1 0 0 -3 5 2 -2 1 -3 -2 1 0 -3 -1 0 -1 -2 -1 -2 0 3 -1 -4 +E -1 0 0 2 -3 2 5 -2 0 -3 -3 1 -2 -3 -1 0 -1 -3 -2 -2 1 4 -1 -4 +G 0 -2 0 -1 -2 -2 -2 6 -2 -3 -4 -1 -2 -3 -2 0 -2 -2 -3 -3 -1 -2 -1 -4 +H -2 0 1 -1 -3 1 0 -2 7 -3 -3 -1 -1 -1 -2 -1 -2 -2 2 -3 0 0 -1 -4 +I -1 -3 -3 -3 -1 -3 -3 -3 -3 4 2 -3 1 0 -3 -2 -1 -2 -1 3 -3 -3 -1 -4 +L -1 -2 -3 -3 -1 -2 -3 -4 -3 2 4 -2 2 0 -3 -2 -1 -2 -1 1 -3 -2 -1 -4 +K -1 2 0 -1 -3 1 1 -1 -1 -3 -2 4 -1 -3 -1 0 -1 -3 -2 -2 0 1 -1 -4 +M -1 -1 -2 -3 -1 0 -2 -2 -1 1 2 -1 5 0 -2 -1 -1 -1 -1 1 -3 -1 -1 -4 +F -2 -3 -3 -3 -2 -3 -3 -3 -1 0 0 -3 0 6 -4 -2 -2 1 3 -1 -3 -3 -1 -4 +P -1 -2 -2 -1 -3 -1 -1 -2 -2 -3 -3 -1 -2 -4 7 -1 -1 -4 -3 -2 -2 -1 -2 -4 +S 1 -1 1 0 -1 0 0 0 -1 -2 -2 0 -1 -2 -1 4 1 -3 -2 -2 0 0 0 -4 +T 0 -1 0 -1 -1 -1 -1 -2 -2 -1 -1 -1 -1 -2 -1 1 4 -2 -2 0 0 -1 0 -4 +W -3 -3 -4 -4 -2 -2 -3 -2 -2 -2 -2 -3 -1 1 -4 -3 -2 10 2 -3 -4 -2 -2 -4 +Y -2 -2 -2 -3 -2 -1 -2 -3 2 -1 -1 -2 -1 3 -3 -2 -2 2 6 -1 -2 -2 -1 -4 +V 0 -2 -3 -3 -1 -2 -2 -3 -3 3 1 -2 1 -1 -2 -2 0 -3 -1 4 -3 -2 -1 -4 +B -2 -1 3 4 -3 0 1 -1 0 -3 -3 0 -3 -3 -2 0 0 -4 -2 -3 4 1 -1 -4 +Z -1 0 0 1 -3 3 4 -2 0 -3 -2 1 -1 -3 -1 0 -1 -2 -2 -2 1 3 -1 -4 +X 0 -1 -1 -1 -2 -1 -1 -1 -1 -1 -1 -1 -1 -1 -2 0 0 -2 -1 -1 -1 -1 -1 -4 +* -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 1 |
| b |
| diff -r 7950e4c52972 -r 22b245c1bb94 Hammock/matrices/blosum62.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/Hammock/matrices/blosum62.txt Fri Jun 23 06:33:16 2017 -0400 |
| b |
| @@ -0,0 +1,31 @@ +# Matrix made by matblas from blosum62.iij +# * column uses minimum score +# BLOSUM Clustered Scoring Matrix in 1/2 Bit Units +# Blocks Database = /data/blocks_5.0/blocks.dat +# Cluster Percentage: >= 62 +# Entropy = 0.6979, Expected = -0.5209 + A R N D C Q E G H I L K M F P S T W Y V B Z X * +A 4 -1 -2 -2 0 -1 -1 0 -2 -1 -1 -1 -1 -2 -1 1 0 -3 -2 0 -2 -1 0 -4 +R -1 5 0 -2 -3 1 0 -2 0 -3 -2 2 -1 -3 -2 -1 -1 -3 -2 -3 -1 0 -1 -4 +N -2 0 6 1 -3 0 0 0 1 -3 -3 0 -2 -3 -2 1 0 -4 -2 -3 3 0 -1 -4 +D -2 -2 1 6 -3 0 2 -1 -1 -3 -4 -1 -3 -3 -1 0 -1 -4 -3 -3 4 1 -1 -4 +C 0 -3 -3 -3 9 -3 -4 -3 -3 -1 -1 -3 -1 -2 -3 -1 -1 -2 -2 -1 -3 -3 -2 -4 +Q -1 1 0 0 -3 5 2 -2 0 -3 -2 1 0 -3 -1 0 -1 -2 -1 -2 0 3 -1 -4 +E -1 0 0 2 -4 2 5 -2 0 -3 -3 1 -2 -3 -1 0 -1 -3 -2 -2 1 4 -1 -4 +G 0 -2 0 -1 -3 -2 -2 6 -2 -4 -4 -2 -3 -3 -2 0 -2 -2 -3 -3 -1 -2 -1 -4 +H -2 0 1 -1 -3 0 0 -2 8 -3 -3 -1 -2 -1 -2 -1 -2 -2 2 -3 0 0 -1 -4 +I -1 -3 -3 -3 -1 -3 -3 -4 -3 4 2 -3 1 0 -3 -2 -1 -3 -1 3 -3 -3 -1 -4 +L -1 -2 -3 -4 -1 -2 -3 -4 -3 2 4 -2 2 0 -3 -2 -1 -2 -1 1 -4 -3 -1 -4 +K -1 2 0 -1 -3 1 1 -2 -1 -3 -2 5 -1 -3 -1 0 -1 -3 -2 -2 0 1 -1 -4 +M -1 -1 -2 -3 -1 0 -2 -3 -2 1 2 -1 5 0 -2 -1 -1 -1 -1 1 -3 -1 -1 -4 +F -2 -3 -3 -3 -2 -3 -3 -3 -1 0 0 -3 0 6 -4 -2 -2 1 3 -1 -3 -3 -1 -4 +P -1 -2 -2 -1 -3 -1 -1 -2 -2 -3 -3 -1 -2 -4 7 -1 -1 -4 -3 -2 -2 -1 -2 -4 +S 1 -1 1 0 -1 0 0 0 -1 -2 -2 0 -1 -2 -1 4 1 -3 -2 -2 0 0 0 -4 +T 0 -1 0 -1 -1 -1 -1 -2 -2 -1 -1 -1 -1 -2 -1 1 5 -2 -2 0 -1 -1 0 -4 +W -3 -3 -4 -4 -2 -2 -3 -2 -2 -3 -2 -3 -1 1 -4 -3 -2 11 2 -3 -4 -3 -2 -4 +Y -2 -2 -2 -3 -2 -1 -2 -3 2 -1 -1 -2 -1 3 -3 -2 -2 2 7 -1 -3 -2 -1 -4 +V 0 -3 -3 -3 -1 -2 -2 -3 -3 3 1 -2 1 -1 -2 -2 0 -3 -1 4 -3 -2 -1 -4 +B -2 -1 3 4 -3 0 1 -1 0 -3 -4 0 -3 -3 -2 0 -1 -4 -3 -3 4 1 -1 -4 +Z -1 0 0 1 -3 3 4 -2 0 -3 -3 1 -1 -3 -1 0 -1 -3 -2 -2 1 4 -1 -4 +X 0 -1 -1 -1 -2 -1 -1 -1 -1 -1 -1 -1 -1 -1 -2 0 0 -2 -1 -1 -1 -1 -1 -4 +* -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 1 |
| b |
| diff -r 7950e4c52972 -r 22b245c1bb94 Hammock/matrices/blosum62.txt~ --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/Hammock/matrices/blosum62.txt~ Fri Jun 23 06:33:16 2017 -0400 |
| b |
| @@ -0,0 +1,31 @@ +# Matrix made by matblas from blosum62.iij +# * column uses minimum score +# BLOSUM Clustered Scoring Matrix in 1/2 Bit Units +# Blocks Database = /data/blocks_5.0/blocks.dat +# Cluster Percentage: >= 62 +# Entropy = 0.6979, Expected = -0.5209 + A R N D C Q E G H I L K M F P S T W Y V B Z X * +A 4 -1 -2 -2 0 -1 -1 0 -2 -1 -1 -1 -1 -2 -1 1 0 -3 -2 0 -2 -1 0 -4 +R -1 5 0 -2 -3 1 0 -2 0 -3 -2 2 -1 -3 -2 -1 -1 -3 -2 -3 -1 0 -1 -4 +N -2 0 6 1 -3 0 0 0 1 -3 -3 0 -2 -3 -2 1 0 -4 -2 -3 3 0 -1 -4 +D -2 -2 1 6 -3 0 2 -1 -1 -3 -4 -1 -3 -3 -1 0 -1 -4 -3 -3 4 1 -1 -4 +C 0 -3 -3 -3 9 -3 -4 -3 -3 -1 -1 -3 -1 -2 -3 -1 -1 -2 -2 -1 -3 -3 -2 -4 +Q -1 1 0 0 -3 5 2 -2 0 -3 -2 1 0 -3 -1 0 -1 -2 -1 -2 0 3 -1 -4 +E -1 0 0 2 -4 2 5 -2 0 -3 -3 1 -2 -3 -1 0 -1 -3 -2 -2 1 4 -1 -4 +G 0 -2 0 -1 -3 -2 -2 6 -2 -4 -4 -2 -3 -3 -2 0 -2 -2 -3 -3 -1 -2 -1 -4 +H -2 0 1 -1 -3 0 0 -2 8 -3 -3 -1 -2 -1 -2 -1 -2 -2 2 -3 0 0 -1 -4 +I -1 -3 -3 -3 -1 -3 -3 -4 -3 4 2 -3 1 0 -3 -2 -1 -3 -1 3 -3 -3 -1 -4 +L -1 -2 -3 -4 -1 -2 -3 -4 -3 2 4 -2 2 0 -3 -2 -1 -2 -1 1 -4 -3 -1 -4 +K -1 2 0 -1 -3 1 1 -2 -1 -3 -2 5 -1 -3 -1 0 -1 -3 -2 -2 0 1 -1 -4 +M -1 -1 -2 -3 -1 0 -2 -3 -2 1 2 -1 5 0 -2 -1 -1 -1 -1 1 -3 -1 -1 -4 +F -2 -3 -3 -3 -2 -3 -3 -3 -1 0 0 -3 0 6 -4 -2 -2 1 3 -1 -3 -3 -1 -4 +P -1 -2 -2 -1 -3 -1 -1 -2 -2 -3 -3 -1 -2 -4 7 -1 -1 -4 -3 -2 -2 -1 -2 -4 +S 1 -1 1 0 -1 0 0 0 -1 -2 -2 0 -1 -2 -1 4 1 -3 -2 -2 0 0 0 -4 +T 0 -1 0 -1 -1 -1 -1 -2 -2 -1 -1 -1 -1 -2 -1 1 5 -2 -2 0 -1 -1 0 -4 +W -3 -3 -4 -4 -2 -2 -3 -2 -2 -3 -2 -3 -1 1 -4 -3 -2 11 2 -3 -4 -3 -2 -4 +Y -2 -2 -2 -3 -2 -1 -2 -3 2 -1 -1 -2 -1 3 -3 -2 -2 2 7 -1 -3 -2 -1 -4 +V 0 -3 -3 -3 -1 -2 -2 -3 -3 3 1 -2 1 -1 -2 -2 0 -3 -1 4 -3 -2 -1 -4 +B -2 -1 3 4 -3 0 1 -1 0 -3 -4 0 -3 -3 -2 0 -1 -4 -3 -3 4 1 -1 -4 +Z -1 0 0 1 -3 3 4 -2 0 -3 -3 1 -1 -3 -1 0 -1 -3 -2 -2 1 4 -1 -4 +X 0 -1 -1 -1 -2 -1 -1 -1 -1 -1 -1 -1 -1 -1 -2 0 0 -2 -1 -1 -1 -1 -1 -4 +* -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 1 |
| b |
| diff -r 7950e4c52972 -r 22b245c1bb94 Hammock/matrices/blosum65.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/Hammock/matrices/blosum65.txt Fri Jun 23 06:33:16 2017 -0400 |
| b |
| @@ -0,0 +1,31 @@ +# Matrix made by matblas from blosum65.iij +# * column uses minimum score +# BLOSUM Clustered Scoring Matrix in 1/2 Bit Units +# Blocks Database = /data/blocks_5.0/blocks.dat +# Cluster Percentage: >= 65 +# Entropy = 0.7576, Expected = -0.5675 + A R N D C Q E G H I L K M F P S T W Y V B Z X * +A 4 -1 -2 -2 0 -1 -1 0 -2 -1 -2 -1 -1 -2 -1 1 0 -3 -2 0 -2 -1 -1 -5 +R -1 6 0 -2 -4 1 0 -2 0 -3 -2 2 -2 -3 -2 -1 -1 -3 -2 -3 -1 0 -1 -5 +N -2 0 6 1 -3 0 0 -1 1 -3 -4 0 -2 -3 -2 1 0 -4 -2 -3 3 0 -1 -5 +D -2 -2 1 6 -4 0 2 -1 -1 -3 -4 -1 -3 -4 -2 0 -1 -5 -3 -3 4 1 -1 -5 +C 0 -4 -3 -4 9 -3 -4 -3 -3 -1 -1 -3 -2 -2 -3 -1 -1 -2 -2 -1 -3 -4 -2 -5 +Q -1 1 0 0 -3 6 2 -2 1 -3 -2 1 0 -3 -1 0 -1 -2 -2 -2 0 3 -1 -5 +E -1 0 0 2 -4 2 5 -2 0 -3 -3 1 -2 -3 -1 0 -1 -3 -2 -3 1 4 -1 -5 +G 0 -2 -1 -1 -3 -2 -2 6 -2 -4 -4 -2 -3 -3 -2 0 -2 -3 -3 -3 -1 -2 -2 -5 +H -2 0 1 -1 -3 1 0 -2 8 -3 -3 -1 -2 -1 -2 -1 -2 -2 2 -3 0 0 -1 -5 +I -1 -3 -3 -3 -1 -3 -3 -4 -3 4 2 -3 1 0 -3 -2 -1 -2 -1 3 -3 -3 -1 -5 +L -2 -2 -4 -4 -1 -2 -3 -4 -3 2 4 -3 2 0 -3 -3 -1 -2 -1 1 -4 -3 -1 -5 +K -1 2 0 -1 -3 1 1 -2 -1 -3 -3 5 -2 -3 -1 0 -1 -3 -2 -2 0 1 -1 -5 +M -1 -2 -2 -3 -2 0 -2 -3 -2 1 2 -2 6 0 -3 -2 -1 -2 -1 1 -3 -2 -1 -5 +F -2 -3 -3 -4 -2 -3 -3 -3 -1 0 0 -3 0 6 -4 -2 -2 1 3 -1 -3 -3 -2 -5 +P -1 -2 -2 -2 -3 -1 -1 -2 -2 -3 -3 -1 -3 -4 8 -1 -1 -4 -3 -2 -2 -1 -2 -5 +S 1 -1 1 0 -1 0 0 0 -1 -2 -3 0 -2 -2 -1 4 1 -3 -2 -2 0 0 -1 -5 +T 0 -1 0 -1 -1 -1 -1 -2 -2 -1 -1 -1 -1 -2 -1 1 5 -3 -2 0 -1 -1 -1 -5 +W -3 -3 -4 -5 -2 -2 -3 -3 -2 -2 -2 -3 -2 1 -4 -3 -3 10 2 -3 -4 -3 -2 -5 +Y -2 -2 -2 -3 -2 -2 -2 -3 2 -1 -1 -2 -1 3 -3 -2 -2 2 7 -1 -3 -2 -1 -5 +V 0 -3 -3 -3 -1 -2 -3 -3 -3 3 1 -2 1 -1 -2 -2 0 -3 -1 4 -3 -2 -1 -5 +B -2 -1 3 4 -3 0 1 -1 0 -3 -4 0 -3 -3 -2 0 -1 -4 -3 -3 4 1 -1 -5 +Z -1 0 0 1 -4 3 4 -2 0 -3 -3 1 -2 -3 -1 0 -1 -3 -2 -2 1 4 -1 -5 +X -1 -1 -1 -1 -2 -1 -1 -2 -1 -1 -1 -1 -1 -2 -2 -1 -1 -2 -1 -1 -1 -1 -1 -5 +* -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 1 |
| b |
| diff -r 7950e4c52972 -r 22b245c1bb94 Hammock/matrices/blosum70.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/Hammock/matrices/blosum70.txt Fri Jun 23 06:33:16 2017 -0400 |
| b |
| @@ -0,0 +1,31 @@ +# Matrix made by matblas from blosum70.iij +# * column uses minimum score +# BLOSUM Clustered Scoring Matrix in 1/2 Bit Units +# Blocks Database = /data/blocks_5.0/blocks.dat +# Cluster Percentage: >= 70 +# Entropy = 0.8391, Expected = -0.6313 + A R N D C Q E G H I L K M F P S T W Y V B Z X * +A 4 -2 -2 -2 -1 -1 -1 0 -2 -2 -2 -1 -1 -2 -1 1 0 -3 -2 0 -2 -1 -1 -5 +R -2 6 -1 -2 -4 1 0 -3 0 -3 -3 2 -2 -3 -2 -1 -1 -3 -2 -3 -1 0 -1 -5 +N -2 -1 6 1 -3 0 0 -1 0 -4 -4 0 -2 -3 -2 0 0 -4 -2 -3 3 0 -1 -5 +D -2 -2 1 6 -4 -1 1 -2 -1 -4 -4 -1 -3 -4 -2 0 -1 -5 -4 -4 4 1 -2 -5 +C -1 -4 -3 -4 9 -3 -4 -3 -4 -1 -2 -4 -2 -2 -3 -1 -1 -3 -3 -1 -4 -4 -2 -5 +Q -1 1 0 -1 -3 6 2 -2 1 -3 -2 1 0 -3 -2 0 -1 -2 -2 -2 0 3 -1 -5 +E -1 0 0 1 -4 2 5 -2 0 -4 -3 1 -2 -4 -1 0 -1 -4 -3 -3 1 4 -1 -5 +G 0 -3 -1 -2 -3 -2 -2 6 -2 -4 -4 -2 -3 -4 -3 -1 -2 -3 -4 -4 -1 -2 -2 -5 +H -2 0 0 -1 -4 1 0 -2 8 -4 -3 -1 -2 -1 -2 -1 -2 -2 2 -3 -1 0 -1 -5 +I -2 -3 -4 -4 -1 -3 -4 -4 -4 4 2 -3 1 0 -3 -3 -1 -3 -1 3 -4 -3 -1 -5 +L -2 -3 -4 -4 -2 -2 -3 -4 -3 2 4 -3 2 0 -3 -3 -2 -2 -1 1 -4 -3 -1 -5 +K -1 2 0 -1 -4 1 1 -2 -1 -3 -3 5 -2 -3 -1 0 -1 -3 -2 -3 -1 1 -1 -5 +M -1 -2 -2 -3 -2 0 -2 -3 -2 1 2 -2 6 0 -3 -2 -1 -2 -1 1 -3 -2 -1 -5 +F -2 -3 -3 -4 -2 -3 -4 -4 -1 0 0 -3 0 6 -4 -3 -2 1 3 -1 -4 -4 -2 -5 +P -1 -2 -2 -2 -3 -2 -1 -3 -2 -3 -3 -1 -3 -4 8 -1 -1 -4 -3 -3 -2 -1 -2 -5 +S 1 -1 0 0 -1 0 0 -1 -1 -3 -3 0 -2 -3 -1 4 1 -3 -2 -2 0 0 -1 -5 +T 0 -1 0 -1 -1 -1 -1 -2 -2 -1 -2 -1 -1 -2 -1 1 5 -3 -2 0 -1 -1 -1 -5 +W -3 -3 -4 -5 -3 -2 -4 -3 -2 -3 -2 -3 -2 1 -4 -3 -3 11 2 -3 -4 -3 -3 -5 +Y -2 -2 -2 -4 -3 -2 -3 -4 2 -1 -1 -2 -1 3 -3 -2 -2 2 7 -2 -3 -2 -2 -5 +V 0 -3 -3 -4 -1 -2 -3 -4 -3 3 1 -3 1 -1 -3 -2 0 -3 -2 4 -3 -3 -1 -5 +B -2 -1 3 4 -4 0 1 -1 -1 -4 -4 -1 -3 -4 -2 0 -1 -4 -3 -3 4 0 -1 -5 +Z -1 0 0 1 -4 3 4 -2 0 -3 -3 1 -2 -4 -1 0 -1 -3 -2 -3 0 4 -1 -5 +X -1 -1 -1 -2 -2 -1 -1 -2 -1 -1 -1 -1 -1 -2 -2 -1 -1 -3 -2 -1 -1 -1 -1 -5 +* -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 1 |
| b |
| diff -r 7950e4c52972 -r 22b245c1bb94 Hammock/matrices/blosum75.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/Hammock/matrices/blosum75.txt Fri Jun 23 06:33:16 2017 -0400 |
| b |
| @@ -0,0 +1,31 @@ +# Matrix made by matblas from blosum75.iij +# * column uses minimum score +# BLOSUM Clustered Scoring Matrix in 1/2 Bit Units +# Blocks Database = /data/blocks_5.0/blocks.dat +# Cluster Percentage: >= 75 +# Entropy = 0.9077, Expected = -0.6845 + A R N D C Q E G H I L K M F P S T W Y V B Z X * +A 4 -2 -2 -2 -1 -1 -1 0 -2 -2 -2 -1 -1 -3 -1 1 0 -3 -2 0 -2 -1 -1 -5 +R -2 6 -1 -2 -4 1 0 -3 0 -3 -3 2 -2 -3 -2 -1 -1 -3 -2 -3 -1 0 -1 -5 +N -2 -1 6 1 -3 0 -1 -1 0 -4 -4 0 -3 -4 -3 0 0 -4 -3 -3 3 0 -1 -5 +D -2 -2 1 6 -4 -1 1 -2 -1 -4 -4 -1 -4 -4 -2 -1 -1 -5 -4 -4 4 1 -2 -5 +C -1 -4 -3 -4 9 -3 -5 -3 -4 -1 -2 -4 -2 -2 -4 -1 -1 -3 -3 -1 -4 -4 -2 -5 +Q -1 1 0 -1 -3 6 2 -2 1 -3 -3 1 0 -4 -2 0 -1 -2 -2 -2 0 3 -1 -5 +E -1 0 -1 1 -5 2 5 -3 0 -4 -4 1 -2 -4 -1 0 -1 -4 -3 -3 1 4 -1 -5 +G 0 -3 -1 -2 -3 -2 -3 6 -2 -5 -4 -2 -3 -4 -3 -1 -2 -3 -4 -4 -1 -2 -2 -5 +H -2 0 0 -1 -4 1 0 -2 8 -4 -3 -1 -2 -2 -2 -1 -2 -2 2 -4 -1 0 -1 -5 +I -2 -3 -4 -4 -1 -3 -4 -5 -4 4 1 -3 1 0 -3 -3 -1 -3 -2 3 -4 -4 -2 -5 +L -2 -3 -4 -4 -2 -3 -4 -4 -3 1 4 -3 2 0 -3 -3 -2 -2 -1 1 -4 -3 -1 -5 +K -1 2 0 -1 -4 1 1 -2 -1 -3 -3 5 -2 -4 -1 0 -1 -4 -2 -3 -1 1 -1 -5 +M -1 -2 -3 -4 -2 0 -2 -3 -2 1 2 -2 6 0 -3 -2 -1 -2 -2 1 -3 -2 -1 -5 +F -3 -3 -4 -4 -2 -4 -4 -4 -2 0 0 -4 0 6 -4 -3 -2 1 3 -1 -4 -4 -2 -5 +P -1 -2 -3 -2 -4 -2 -1 -3 -2 -3 -3 -1 -3 -4 8 -1 -1 -5 -4 -3 -2 -2 -2 -5 +S 1 -1 0 -1 -1 0 0 -1 -1 -3 -3 0 -2 -3 -1 5 1 -3 -2 -2 0 0 -1 -5 +T 0 -1 0 -1 -1 -1 -1 -2 -2 -1 -2 -1 -1 -2 -1 1 5 -3 -2 0 -1 -1 -1 -5 +W -3 -3 -4 -5 -3 -2 -4 -3 -2 -3 -2 -4 -2 1 -5 -3 -3 11 2 -3 -5 -3 -3 -5 +Y -2 -2 -3 -4 -3 -2 -3 -4 2 -2 -1 -2 -2 3 -4 -2 -2 2 7 -2 -3 -3 -2 -5 +V 0 -3 -3 -4 -1 -2 -3 -4 -4 3 1 -3 1 -1 -3 -2 0 -3 -2 4 -4 -3 -1 -5 +B -2 -1 3 4 -4 0 1 -1 -1 -4 -4 -1 -3 -4 -2 0 -1 -5 -3 -4 4 0 -2 -5 +Z -1 0 0 1 -4 3 4 -2 0 -4 -3 1 -2 -4 -2 0 -1 -3 -3 -3 0 4 -1 -5 +X -1 -1 -1 -2 -2 -1 -1 -2 -1 -2 -1 -1 -1 -2 -2 -1 -1 -3 -2 -1 -2 -1 -1 -5 +* -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 1 |
| b |
| diff -r 7950e4c52972 -r 22b245c1bb94 Hammock/matrices/blosum80.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/Hammock/matrices/blosum80.txt Fri Jun 23 06:33:16 2017 -0400 |
| b |
| @@ -0,0 +1,31 @@ +# Matrix made by matblas from blosum80_3.iij +# * column uses minimum score +# BLOSUM Clustered Scoring Matrix in 1/3 Bit Units +# Blocks Database = /data/blocks_5.0/blocks.dat +# Cluster Percentage: >= 80 +# Entropy = 0.9868, Expected = -0.7442 + A R N D C Q E G H I L K M F P S T W Y V B Z X * +A 7 -3 -3 -3 -1 -2 -2 0 -3 -3 -3 -1 -2 -4 -1 2 0 -5 -4 -1 -3 -2 -1 -8 +R -3 9 -1 -3 -6 1 -1 -4 0 -5 -4 3 -3 -5 -3 -2 -2 -5 -4 -4 -2 0 -2 -8 +N -3 -1 9 2 -5 0 -1 -1 1 -6 -6 0 -4 -6 -4 1 0 -7 -4 -5 5 -1 -2 -8 +D -3 -3 2 10 -7 -1 2 -3 -2 -7 -7 -2 -6 -6 -3 -1 -2 -8 -6 -6 6 1 -3 -8 +C -1 -6 -5 -7 13 -5 -7 -6 -7 -2 -3 -6 -3 -4 -6 -2 -2 -5 -5 -2 -6 -7 -4 -8 +Q -2 1 0 -1 -5 9 3 -4 1 -5 -4 2 -1 -5 -3 -1 -1 -4 -3 -4 -1 5 -2 -8 +E -2 -1 -1 2 -7 3 8 -4 0 -6 -6 1 -4 -6 -2 -1 -2 -6 -5 -4 1 6 -2 -8 +G 0 -4 -1 -3 -6 -4 -4 9 -4 -7 -7 -3 -5 -6 -5 -1 -3 -6 -6 -6 -2 -4 -3 -8 +H -3 0 1 -2 -7 1 0 -4 12 -6 -5 -1 -4 -2 -4 -2 -3 -4 3 -5 -1 0 -2 -8 +I -3 -5 -6 -7 -2 -5 -6 -7 -6 7 2 -5 2 -1 -5 -4 -2 -5 -3 4 -6 -6 -2 -8 +L -3 -4 -6 -7 -3 -4 -6 -7 -5 2 6 -4 3 0 -5 -4 -3 -4 -2 1 -7 -5 -2 -8 +K -1 3 0 -2 -6 2 1 -3 -1 -5 -4 8 -3 -5 -2 -1 -1 -6 -4 -4 -1 1 -2 -8 +M -2 -3 -4 -6 -3 -1 -4 -5 -4 2 3 -3 9 0 -4 -3 -1 -3 -3 1 -5 -3 -2 -8 +F -4 -5 -6 -6 -4 -5 -6 -6 -2 -1 0 -5 0 10 -6 -4 -4 0 4 -2 -6 -6 -3 -8 +P -1 -3 -4 -3 -6 -3 -2 -5 -4 -5 -5 -2 -4 -6 12 -2 -3 -7 -6 -4 -4 -2 -3 -8 +S 2 -2 1 -1 -2 -1 -1 -1 -2 -4 -4 -1 -3 -4 -2 7 2 -6 -3 -3 0 -1 -1 -8 +T 0 -2 0 -2 -2 -1 -2 -3 -3 -2 -3 -1 -1 -4 -3 2 8 -5 -3 0 -1 -2 -1 -8 +W -5 -5 -7 -8 -5 -4 -6 -6 -4 -5 -4 -6 -3 0 -7 -6 -5 16 3 -5 -8 -5 -5 -8 +Y -4 -4 -4 -6 -5 -3 -5 -6 3 -3 -2 -4 -3 4 -6 -3 -3 3 11 -3 -5 -4 -3 -8 +V -1 -4 -5 -6 -2 -4 -4 -6 -5 4 1 -4 1 -2 -4 -3 0 -5 -3 7 -6 -4 -2 -8 +B -3 -2 5 6 -6 -1 1 -2 -1 -6 -7 -1 -5 -6 -4 0 -1 -8 -5 -6 6 0 -3 -8 +Z -2 0 -1 1 -7 5 6 -4 0 -6 -5 1 -3 -6 -2 -1 -2 -5 -4 -4 0 6 -1 -8 +X -1 -2 -2 -3 -4 -2 -2 -3 -2 -2 -2 -2 -2 -3 -3 -1 -1 -5 -3 -2 -3 -1 -2 -8 +* -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 1 |
| b |
| diff -r 7950e4c52972 -r 22b245c1bb94 Hammock/matrices/blosum85.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/Hammock/matrices/blosum85.txt Fri Jun 23 06:33:16 2017 -0400 |
| b |
| @@ -0,0 +1,31 @@ +# Matrix made by matblas from blosum85.iij +# * column uses minimum score +# BLOSUM Clustered Scoring Matrix in 1/2 Bit Units +# Blocks Database = /data/blocks_5.0/blocks.dat +# Cluster Percentage: >= 85 +# Entropy = 1.0805, Expected = -0.8153 + A R N D C Q E G H I L K M F P S T W Y V B Z X * +A 5 -2 -2 -2 -1 -1 -1 0 -2 -2 -2 -1 -2 -3 -1 1 0 -3 -3 -1 -2 -1 -1 -6 +R -2 6 -1 -2 -4 1 -1 -3 0 -4 -3 2 -2 -4 -2 -1 -2 -4 -3 -3 -2 0 -2 -6 +N -2 -1 7 1 -4 0 -1 -1 0 -4 -4 0 -3 -4 -3 0 0 -5 -3 -4 4 -1 -2 -6 +D -2 -2 1 7 -5 -1 1 -2 -2 -5 -5 -1 -4 -4 -2 -1 -2 -6 -4 -4 4 1 -2 -6 +C -1 -4 -4 -5 9 -4 -5 -4 -5 -2 -2 -4 -2 -3 -4 -2 -2 -4 -3 -1 -4 -5 -3 -6 +Q -1 1 0 -1 -4 6 2 -3 1 -4 -3 1 0 -4 -2 -1 -1 -3 -2 -3 -1 4 -1 -6 +E -1 -1 -1 1 -5 2 6 -3 -1 -4 -4 0 -3 -4 -2 -1 -1 -4 -4 -3 0 4 -1 -6 +G 0 -3 -1 -2 -4 -3 -3 6 -3 -5 -5 -2 -4 -4 -3 -1 -2 -4 -5 -4 -1 -3 -2 -6 +H -2 0 0 -2 -5 1 -1 -3 8 -4 -3 -1 -3 -2 -3 -1 -2 -3 2 -4 -1 0 -2 -6 +I -2 -4 -4 -5 -2 -4 -4 -5 -4 5 1 -3 1 -1 -4 -3 -1 -3 -2 3 -5 -4 -2 -6 +L -2 -3 -4 -5 -2 -3 -4 -5 -3 1 4 -3 2 0 -4 -3 -2 -3 -2 0 -5 -4 -2 -6 +K -1 2 0 -1 -4 1 0 -2 -1 -3 -3 6 -2 -4 -2 -1 -1 -5 -3 -3 -1 1 -1 -6 +M -2 -2 -3 -4 -2 0 -3 -4 -3 1 2 -2 7 -1 -3 -2 -1 -2 -2 0 -4 -2 -1 -6 +F -3 -4 -4 -4 -3 -4 -4 -4 -2 -1 0 -4 -1 7 -4 -3 -3 0 3 -1 -4 -4 -2 -6 +P -1 -2 -3 -2 -4 -2 -2 -3 -3 -4 -4 -2 -3 -4 8 -1 -2 -5 -4 -3 -3 -2 -2 -6 +S 1 -1 0 -1 -2 -1 -1 -1 -1 -3 -3 -1 -2 -3 -1 5 1 -4 -2 -2 0 -1 -1 -6 +T 0 -2 0 -2 -2 -1 -1 -2 -2 -1 -2 -1 -1 -3 -2 1 5 -4 -2 0 -1 -1 -1 -6 +W -3 -4 -5 -6 -4 -3 -4 -4 -3 -3 -3 -5 -2 0 -5 -4 -4 11 2 -3 -5 -4 -3 -6 +Y -3 -3 -3 -4 -3 -2 -4 -5 2 -2 -2 -3 -2 3 -4 -2 -2 2 7 -2 -4 -3 -2 -6 +V -1 -3 -4 -4 -1 -3 -3 -4 -4 3 0 -3 0 -1 -3 -2 0 -3 -2 5 -4 -3 -1 -6 +B -2 -2 4 4 -4 -1 0 -1 -1 -5 -5 -1 -4 -4 -3 0 -1 -5 -4 -4 4 0 -2 -6 +Z -1 0 -1 1 -5 4 4 -3 0 -4 -4 1 -2 -4 -2 -1 -1 -4 -3 -3 0 4 -1 -6 +X -1 -2 -2 -2 -3 -1 -1 -2 -2 -2 -2 -1 -1 -2 -2 -1 -1 -3 -2 -1 -2 -1 -2 -6 +* -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 1 |
| b |
| diff -r 7950e4c52972 -r 22b245c1bb94 Hammock/matrices/blosum90.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/Hammock/matrices/blosum90.txt Fri Jun 23 06:33:16 2017 -0400 |
| b |
| @@ -0,0 +1,31 @@ +# Matrix made by matblas from blosum90.iij +# * column uses minimum score +# BLOSUM Clustered Scoring Matrix in 1/2 Bit Units +# Blocks Database = /data/blocks_5.0/blocks.dat +# Cluster Percentage: >= 90 +# Entropy = 1.1806, Expected = -0.8887 + A R N D C Q E G H I L K M F P S T W Y V B Z X * +A 5 -2 -2 -3 -1 -1 -1 0 -2 -2 -2 -1 -2 -3 -1 1 0 -4 -3 -1 -2 -1 -1 -6 +R -2 6 -1 -3 -5 1 -1 -3 0 -4 -3 2 -2 -4 -3 -1 -2 -4 -3 -3 -2 0 -2 -6 +N -2 -1 7 1 -4 0 -1 -1 0 -4 -4 0 -3 -4 -3 0 0 -5 -3 -4 4 -1 -2 -6 +D -3 -3 1 7 -5 -1 1 -2 -2 -5 -5 -1 -4 -5 -3 -1 -2 -6 -4 -5 4 0 -2 -6 +C -1 -5 -4 -5 9 -4 -6 -4 -5 -2 -2 -4 -2 -3 -4 -2 -2 -4 -4 -2 -4 -5 -3 -6 +Q -1 1 0 -1 -4 7 2 -3 1 -4 -3 1 0 -4 -2 -1 -1 -3 -3 -3 -1 4 -1 -6 +E -1 -1 -1 1 -6 2 6 -3 -1 -4 -4 0 -3 -5 -2 -1 -1 -5 -4 -3 0 4 -2 -6 +G 0 -3 -1 -2 -4 -3 -3 6 -3 -5 -5 -2 -4 -5 -3 -1 -3 -4 -5 -5 -2 -3 -2 -6 +H -2 0 0 -2 -5 1 -1 -3 8 -4 -4 -1 -3 -2 -3 -2 -2 -3 1 -4 -1 0 -2 -6 +I -2 -4 -4 -5 -2 -4 -4 -5 -4 5 1 -4 1 -1 -4 -3 -1 -4 -2 3 -5 -4 -2 -6 +L -2 -3 -4 -5 -2 -3 -4 -5 -4 1 5 -3 2 0 -4 -3 -2 -3 -2 0 -5 -4 -2 -6 +K -1 2 0 -1 -4 1 0 -2 -1 -4 -3 6 -2 -4 -2 -1 -1 -5 -3 -3 -1 1 -1 -6 +M -2 -2 -3 -4 -2 0 -3 -4 -3 1 2 -2 7 -1 -3 -2 -1 -2 -2 0 -4 -2 -1 -6 +F -3 -4 -4 -5 -3 -4 -5 -5 -2 -1 0 -4 -1 7 -4 -3 -3 0 3 -2 -4 -4 -2 -6 +P -1 -3 -3 -3 -4 -2 -2 -3 -3 -4 -4 -2 -3 -4 8 -2 -2 -5 -4 -3 -3 -2 -2 -6 +S 1 -1 0 -1 -2 -1 -1 -1 -2 -3 -3 -1 -2 -3 -2 5 1 -4 -3 -2 0 -1 -1 -6 +T 0 -2 0 -2 -2 -1 -1 -3 -2 -1 -2 -1 -1 -3 -2 1 6 -4 -2 -1 -1 -1 -1 -6 +W -4 -4 -5 -6 -4 -3 -5 -4 -3 -4 -3 -5 -2 0 -5 -4 -4 11 2 -3 -6 -4 -3 -6 +Y -3 -3 -3 -4 -4 -3 -4 -5 1 -2 -2 -3 -2 3 -4 -3 -2 2 8 -3 -4 -3 -2 -6 +V -1 -3 -4 -5 -2 -3 -3 -5 -4 3 0 -3 0 -2 -3 -2 -1 -3 -3 5 -4 -3 -2 -6 +B -2 -2 4 4 -4 -1 0 -2 -1 -5 -5 -1 -4 -4 -3 0 -1 -6 -4 -4 4 0 -2 -6 +Z -1 0 -1 0 -5 4 4 -3 0 -4 -4 1 -2 -4 -2 -1 -1 -4 -3 -3 0 4 -1 -6 +X -1 -2 -2 -2 -3 -1 -2 -2 -2 -2 -2 -1 -1 -2 -2 -1 -1 -3 -2 -2 -2 -1 -2 -6 +* -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 1 |
| b |
| diff -r 7950e4c52972 -r 22b245c1bb94 Hammock/matrices/gonnet250.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/Hammock/matrices/gonnet250.txt Fri Jun 23 06:33:16 2017 -0400 |
| b |
| @@ -0,0 +1,26 @@ +# PAM 250 matrix recommended by Gonnet, Cohen & Benner +# Science June 5, 1992. +# Values rounded to nearest integer + C S T P A G N D E Q H R K M I L V F Y W X * +C 12 0 0 -3 0 -2 -2 -3 -3 -2 -1 -2 -3 -1 -1 -2 0 -1 0 -1 -3 -8 +S 0 2 2 0 1 0 1 0 0 0 0 0 0 -1 -2 -2 -1 -3 -2 -3 0 -8 +T 0 2 2 0 1 -1 0 0 0 0 0 0 0 -1 -1 -1 0 -2 -2 -4 0 -8 +P -3 0 0 8 0 -2 -1 -1 0 0 -1 -1 -1 -2 -3 -2 -2 -4 -3 -5 -1 -8 +A 0 1 1 0 2 0 0 0 0 0 -1 -1 0 -1 -1 -1 0 -2 -2 -4 0 -8 +G -2 0 -1 -2 0 7 0 0 -1 -1 -1 -1 -1 -4 -4 -4 -3 -5 -4 -4 -1 -8 +N -2 1 0 -1 0 0 4 2 1 1 1 0 1 -2 -3 -3 -2 -3 -1 -4 0 -8 +D -3 0 0 -1 0 0 2 5 3 1 0 0 0 -3 -4 -4 -3 -4 -3 -5 -1 -8 +E -3 0 0 0 0 -1 1 3 4 2 0 0 1 -2 -3 -3 -2 -4 -3 -4 -1 -8 +Q -2 0 0 0 0 -1 1 1 2 3 1 2 2 -1 -2 -2 -2 -3 -2 -3 -1 -8 +H -1 0 0 -1 -1 -1 1 0 0 1 6 1 1 -1 -2 -2 -2 0 2 -1 -1 -8 +R -2 0 0 -1 -1 -1 0 0 0 2 1 5 3 -2 -2 -2 -2 -3 -2 -2 -1 -8 +K -3 0 0 -1 0 -1 1 0 1 2 1 3 3 -1 -2 -2 -2 -3 -2 -4 -1 -8 +M -1 -1 -1 -2 -1 -4 -2 -3 -2 -1 -1 -2 -1 4 2 3 2 2 0 -1 -1 -8 +I -1 -2 -1 -3 -1 -4 -3 -4 -3 -2 -2 -2 -2 2 4 3 3 1 -1 -2 -1 -8 +L -2 -2 -1 -2 -1 -4 -3 -4 -3 -2 -2 -2 -2 3 3 4 2 2 0 -1 -1 -8 +V 0 -1 0 -2 0 -3 -2 -3 -2 -2 -2 -2 -2 2 3 2 3 0 -1 -3 -1 -8 +F -1 -3 -2 -4 -2 -5 -3 -4 -4 -3 0 -3 -3 2 1 2 0 7 5 4 -2 -8 +Y 0 -2 -2 -3 -2 -4 -1 -3 -3 -2 2 -2 -2 0 -1 0 -1 5 8 4 -2 -8 +W -1 -3 -4 -5 -4 -4 -4 -5 -4 -3 -1 -2 -4 -1 -2 -1 -3 4 4 14 -4 -8 +X -3 0 0 -1 0 -1 0 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -2 -2 -4 -1 -8 +* -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 1 |
| b |
| diff -r 7950e4c52972 -r 22b245c1bb94 Hammock/matrices/mcla71.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/Hammock/matrices/mcla71.txt Fri Jun 23 06:33:16 2017 -0400 |
| b |
| @@ -0,0 +1,22 @@ +# McLachlan 1971 + A R N D C Q E G H I L K M F P S T W Y V +A 8 2 3 3 1 3 4 3 3 2 2 3 3 1 4 4 3 1 1 3 +R 2 8 3 1 1 5 3 3 5 1 2 5 1 1 3 4 3 3 2 2 +N 3 3 8 5 1 4 4 3 4 1 1 4 2 0 1 5 3 0 2 1 +D 3 1 5 8 1 4 5 3 4 0 1 3 2 1 3 3 3 0 1 1 +C 1 1 1 1 9 0 0 1 3 1 0 0 3 0 0 2 2 2 1 1 +Q 3 5 4 4 0 8 5 2 4 0 3 4 3 0 3 4 3 2 1 2 +E 4 3 4 5 0 5 8 3 2 1 1 4 1 0 4 4 4 1 2 2 +G 3 3 3 3 1 2 3 8 2 1 1 3 1 0 3 3 2 1 0 2 +H 3 5 4 4 3 4 2 2 8 2 2 4 3 4 3 3 4 3 4 2 +I 2 1 1 0 1 0 1 1 2 8 5 1 5 3 1 2 3 3 3 5 +L 2 2 1 1 0 3 1 1 2 5 8 2 6 5 1 2 3 3 3 5 +K 3 5 4 3 0 4 4 3 4 1 2 8 1 0 3 3 3 1 1 2 +M 3 1 2 2 3 3 1 1 3 5 6 1 8 5 1 2 3 1 2 4 +F 1 1 0 1 0 0 0 0 4 3 5 0 5 9 1 2 1 6 6 3 +P 4 3 1 3 0 3 4 3 3 1 1 3 1 1 8 3 3 0 0 2 +S 4 4 5 3 2 4 4 3 3 2 2 3 2 2 3 8 5 3 3 2 +T 3 3 3 3 2 3 4 2 4 3 3 3 3 1 3 5 8 2 1 3 +W 1 3 0 0 2 2 1 1 3 3 3 1 1 6 0 3 2 9 6 2 +Y 1 2 2 1 1 1 2 0 4 3 3 1 2 6 0 3 1 6 9 3 +V 3 2 1 1 1 2 2 2 2 5 5 2 4 3 2 2 3 2 3 8 |
| b |
| diff -r 7950e4c52972 -r 22b245c1bb94 Hammock/matrices/pam250.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/Hammock/matrices/pam250.txt Fri Jun 23 06:33:16 2017 -0400 |
| [ |
| @@ -0,0 +1,34 @@ +# +# This matrix was produced by "pam" Version 1.0.6 [28-Jul-93] +# +# PAM 250 substitution matrix, scale = ln(2)/3 = 0.231049 +# +# Expected score = -0.844, Entropy = 0.354 bits +# +# Lowest score = -8, Highest score = 17 +# + A R N D C Q E G H I L K M F P S T W Y V B Z X * +A 2 -2 0 0 -2 0 0 1 -1 -1 -2 -1 -1 -3 1 1 1 -6 -3 0 0 0 0 -8 +R -2 6 0 -1 -4 1 -1 -3 2 -2 -3 3 0 -4 0 0 -1 2 -4 -2 -1 0 -1 -8 +N 0 0 2 2 -4 1 1 0 2 -2 -3 1 -2 -3 0 1 0 -4 -2 -2 2 1 0 -8 +D 0 -1 2 4 -5 2 3 1 1 -2 -4 0 -3 -6 -1 0 0 -7 -4 -2 3 3 -1 -8 +C -2 -4 -4 -5 12 -5 -5 -3 -3 -2 -6 -5 -5 -4 -3 0 -2 -8 0 -2 -4 -5 -3 -8 +Q 0 1 1 2 -5 4 2 -1 3 -2 -2 1 -1 -5 0 -1 -1 -5 -4 -2 1 3 -1 -8 +E 0 -1 1 3 -5 2 4 0 1 -2 -3 0 -2 -5 -1 0 0 -7 -4 -2 3 3 -1 -8 +G 1 -3 0 1 -3 -1 0 5 -2 -3 -4 -2 -3 -5 0 1 0 -7 -5 -1 0 0 -1 -8 +H -1 2 2 1 -3 3 1 -2 6 -2 -2 0 -2 -2 0 -1 -1 -3 0 -2 1 2 -1 -8 +I -1 -2 -2 -2 -2 -2 -2 -3 -2 5 2 -2 2 1 -2 -1 0 -5 -1 4 -2 -2 -1 -8 +L -2 -3 -3 -4 -6 -2 -3 -4 -2 2 6 -3 4 2 -3 -3 -2 -2 -1 2 -3 -3 -1 -8 +K -1 3 1 0 -5 1 0 -2 0 -2 -3 5 0 -5 -1 0 0 -3 -4 -2 1 0 -1 -8 +M -1 0 -2 -3 -5 -1 -2 -3 -2 2 4 0 6 0 -2 -2 -1 -4 -2 2 -2 -2 -1 -8 +F -3 -4 -3 -6 -4 -5 -5 -5 -2 1 2 -5 0 9 -5 -3 -3 0 7 -1 -4 -5 -2 -8 +P 1 0 0 -1 -3 0 -1 0 0 -2 -3 -1 -2 -5 6 1 0 -6 -5 -1 -1 0 -1 -8 +S 1 0 1 0 0 -1 0 1 -1 -1 -3 0 -2 -3 1 2 1 -2 -3 -1 0 0 0 -8 +T 1 -1 0 0 -2 -1 0 0 -1 0 -2 0 -1 -3 0 1 3 -5 -3 0 0 -1 0 -8 +W -6 2 -4 -7 -8 -5 -7 -7 -3 -5 -2 -3 -4 0 -6 -2 -5 17 0 -6 -5 -6 -4 -8 +Y -3 -4 -2 -4 0 -4 -4 -5 0 -1 -1 -4 -2 7 -5 -3 -3 0 10 -2 -3 -4 -2 -8 +V 0 -2 -2 -2 -2 -2 -2 -1 -2 4 2 -2 2 -1 -1 -1 0 -6 -2 4 -2 -2 -1 -8 +B 0 -1 2 3 -4 1 3 0 1 -2 -3 1 -2 -4 -1 0 0 -5 -3 -2 3 2 -1 -8 +Z 0 0 1 3 -5 3 3 0 2 -2 -3 0 -2 -5 0 0 -1 -6 -4 -2 2 3 -1 -8 +X 0 -1 0 -1 -3 -1 -1 -1 -1 -1 -1 -1 -1 -2 -1 0 0 -4 -2 -1 -1 -1 -1 -8 +* -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 1 |
| b |
| diff -r 7950e4c52972 -r 22b245c1bb94 Hammock/settings/misc/blosum62.freq_rownorm --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/Hammock/settings/misc/blosum62.freq_rownorm Fri Jun 23 06:33:16 2017 -0400 |
| b |
| @@ -0,0 +1,25 @@ +# BLOSUM Clustered Target Frequencies=qij +# Blocks Database = /data/blocks_5.0/blocks.dat +# Cluster Percentage: >= 62 +# Normalized frequencies (by row) from file: blosum62.qij +A R N D C Q E G H I L K M F P S T W Y V +0.2901 0.0310 0.0256 0.0297 0.0216 0.0256 0.0405 0.0783 0.0148 0.0432 0.0594 0.0445 0.0175 0.0216 0.0297 0.0850 0.0499 0.0054 0.0175 0.0688 +0.0446 0.3450 0.0388 0.0310 0.0078 0.0484 0.0523 0.0329 0.0233 0.0233 0.0465 0.1202 0.0155 0.0174 0.0194 0.0446 0.0349 0.0058 0.0174 0.0310 +0.0427 0.0449 0.3169 0.0831 0.0090 0.0337 0.0494 0.0652 0.0315 0.0225 0.0315 0.0539 0.0112 0.0180 0.0202 0.0697 0.0494 0.0045 0.0157 0.0270 +0.0410 0.0299 0.0690 0.3974 0.0075 0.0299 0.0914 0.0466 0.0187 0.0224 0.0280 0.0448 0.0093 0.0149 0.0224 0.0522 0.0354 0.0037 0.0112 0.0243 +0.0650 0.0163 0.0163 0.0163 0.4837 0.0122 0.0163 0.0325 0.0081 0.0447 0.0650 0.0203 0.0163 0.0203 0.0163 0.0407 0.0366 0.0041 0.0122 0.0569 +0.0559 0.0735 0.0441 0.0471 0.0088 0.2147 0.1029 0.0412 0.0294 0.0265 0.0471 0.0912 0.0206 0.0147 0.0235 0.0559 0.0412 0.0059 0.0206 0.0353 +0.0552 0.0497 0.0405 0.0902 0.0074 0.0645 0.2965 0.0350 0.0258 0.0221 0.0368 0.0755 0.0129 0.0166 0.0258 0.0552 0.0368 0.0055 0.0166 0.0313 +0.0783 0.0229 0.0391 0.0337 0.0108 0.0189 0.0256 0.5101 0.0135 0.0189 0.0283 0.0337 0.0094 0.0162 0.0189 0.0513 0.0297 0.0054 0.0108 0.0243 +0.0420 0.0458 0.0534 0.0382 0.0076 0.0382 0.0534 0.0382 0.3550 0.0229 0.0382 0.0458 0.0153 0.0305 0.0191 0.0420 0.0267 0.0076 0.0573 0.0229 +0.0471 0.0177 0.0147 0.0177 0.0162 0.0133 0.0177 0.0206 0.0088 0.2710 0.1679 0.0236 0.0368 0.0442 0.0147 0.0250 0.0398 0.0059 0.0206 0.1767 +0.0445 0.0243 0.0142 0.0152 0.0162 0.0162 0.0202 0.0213 0.0101 0.1154 0.3755 0.0253 0.0496 0.0547 0.0142 0.0243 0.0334 0.0071 0.0223 0.0962 +0.0570 0.1071 0.0415 0.0415 0.0086 0.0535 0.0708 0.0432 0.0207 0.0276 0.0432 0.2781 0.0155 0.0155 0.0276 0.0535 0.0397 0.0052 0.0173 0.0328 +0.0522 0.0321 0.0201 0.0201 0.0161 0.0281 0.0281 0.0281 0.0161 0.1004 0.1968 0.0361 0.1606 0.0482 0.0161 0.0361 0.0402 0.0080 0.0241 0.0924 +0.0338 0.0190 0.0169 0.0169 0.0106 0.0106 0.0190 0.0254 0.0169 0.0634 0.1142 0.0190 0.0254 0.3869 0.0106 0.0254 0.0254 0.0169 0.0888 0.0550 +0.0568 0.0258 0.0233 0.0310 0.0103 0.0207 0.0362 0.0362 0.0129 0.0258 0.0362 0.0413 0.0103 0.0129 0.4935 0.0439 0.0362 0.0026 0.0129 0.0310 +0.1099 0.0401 0.0541 0.0489 0.0175 0.0332 0.0524 0.0663 0.0192 0.0297 0.0419 0.0541 0.0157 0.0209 0.0297 0.2199 0.0820 0.0052 0.0175 0.0419 +0.0730 0.0355 0.0434 0.0375 0.0178 0.0276 0.0394 0.0434 0.0138 0.0533 0.0651 0.0454 0.0197 0.0237 0.0276 0.0927 0.2465 0.0059 0.0178 0.0710 +0.0303 0.0227 0.0152 0.0152 0.0076 0.0152 0.0227 0.0303 0.0152 0.0303 0.0530 0.0227 0.0152 0.0606 0.0076 0.0227 0.0227 0.4924 0.0682 0.0303 +0.0405 0.0280 0.0218 0.0187 0.0093 0.0218 0.0280 0.0249 0.0467 0.0436 0.0685 0.0312 0.0187 0.1308 0.0156 0.0312 0.0280 0.0280 0.3178 0.0467 +0.0700 0.0219 0.0165 0.0178 0.0192 0.0165 0.0233 0.0247 0.0082 0.1646 0.1303 0.0261 0.0316 0.0357 0.0165 0.0329 0.0494 0.0055 0.0206 0.2689 |
| b |
| diff -r 7950e4c52972 -r 22b245c1bb94 Hammock/settings/settings.prop --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/Hammock/settings/settings.prop Fri Jun 23 06:33:16 2017 -0400 |
| [ |
| @@ -0,0 +1,25 @@ +#Lines starting with hash (#) are ignored +#Tool commands. Define full paths if needed. By default (not specified) means locations relative to .jar file in Hammock/dist foltder +#clustalOmegaCommand= +#hmmbuildCommand= +#hmmsearchCommand= +#hhmakeCommand= +#hhsearchCommand= +#reformatCommand= +#Directory for all temporal files. Define full path if needed. Default (not specified): /tmp +#tempDirectory= +#Temporal files subdirectories. Define full paths if needed. Default (not specified): directories in tempDirectory/Hammock_temp/[time]/ +#fastaDirectory= +#msaDirectory= +#hmmDirectory= +#hhDirectory= +#hmmsearchOutDirectory= +#hhsearchOutDirectory= +#fastaDatabaseFile= +#Tool parameters. Generally, it is not recommended to change this section. +clustalOmegaParameters= +hmmbuildParameters=--enone --fragthresh 1.0 --hand --wnone --amino --seed 42 +hmmsearchParameters=--nobias --F1 0.5 --F2 0.05 --F3 1e-2 --nonull2 --seed 42 +hmmalignParameters=--outformat selex --amino --seed 42 +hhmakeParameters=-M a2m -id 100 -diff inf -pcm 3 -nocontxt -v 0 +hhsearchParameters=-norealign -alt 1 -corr 0 -shift 0 -ssm 0 -tags -nocons -nopred -nodssp -sc 0 -v 0 -z 2 -Z 500000 -local -p 0.0 -vit -b 100.0 -E 100.0 -e 100.0 -z 100 |
| b |
| diff -r 7950e4c52972 -r 22b245c1bb94 Hammock/settings/settings.prop~ --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/Hammock/settings/settings.prop~ Fri Jun 23 06:33:16 2017 -0400 |
| b |
| @@ -0,0 +1,11 @@ +#Change "default" to full path if needed. Default means locations relative to .jar file in PhageClust/dist foltder +#clustalOmegaCommand= +#fastaDirectory= +#msaDirectory= +clustalOmegaParameters=--iter=5 --full-iter +hmmbuildParameters=--enone --fragthresh 1.0 --symfrac 0.6 +hmmsearchParameters=--nobias --F1 0.5 --F2 0.05 --F3 1e-2 +hhmakeParameters=-M a2m -id 100 -qsc -100 -pcm 3 +hhalignParameters=-realign -id 100 -diff inf -alt 1 -corr 0 -shift 0 -ssm 0 -nocontxt -pcm 2 -tags -nocons -nopred -nodssp -M a2m -alt 1 -sc 0 -v 0 -z 2 -Z 20 -local -mact 0.0 +hhsearchParameters=-realign -id 100 -diff inf -alt 1 -corr 0 -shift 0 -ssm 0 -nocontxt -pcm 2 -tags -nocons -nopred -nodssp -M a2m -alt 1 -sc 0 -v 0 -z 2 -Z 500 -local -mact 0.0 -p 0 +reformatParameters=-M 30 |
| b |
| diff -r 7950e4c52972 -r 22b245c1bb94 hammock.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/hammock.xml Fri Jun 23 06:33:16 2017 -0400 |
| b |
| b'@@ -0,0 +1,384 @@\n+<tool id="hammock_1.0" name="Hammock - cluster peptides" version="1.1.0" hidden="false">\n+\n+ <description>Clusters short peptide sequences</description>\n+\n+ <command interpreter="bash">\n+wrapper.sh \\$HAMMOCK_JAR full --galaxy -t \\${GALAXY_SLOTS:-4} -i $input --goc $output_clusters --gos $output_sequences --goo $output_sequences_ordered\n+\n+\t #if $label_params.set_labels == "set":\n+ #for $s in $label_params.round_labels:\n+\t\t\t#set $l_field = $l_field + str($s.label) + ","\n+\t\t#end for\t\t\n+\t\t-l $l_field\n+\t #end if\n+\n+\t #if $advanced_initial_params.set_initial_params == "set":\n+\t\t-x $advanced_initial_params.max_shift\n+\t\t-p $advanced_initial_params.shift_penalty\n+\t\t-R $advanced_initial_params.set_order.order\n+\n+\t\t#if $advanced_initial_params.algorithm == "clinkage":\n+\t\t\t--use_clinkage\n+\t\t#end if\n+\n+\t\t#if $advanced_initial_params.algorithm == "greedy":\n+\t\t\t--use_greedy\n+\t\t#end if\n+\n+\t\t#if $advanced_initial_params.set_order.order == "random":\n+\t\t\t-S $advanced_initial_params.set_order.seed\n+\t\t#end if\n+\t\n+\t\t-m \\${MATRIX_PATH}${advanced_initial_params.scoring_matrix}.txt\n+ \t#if $advanced_initial_params.initial_params.set_initial == "set":\n+ \t-g $advanced_initial_params.initial_params.initial_threshold\n+ \t#end if\n+ #end if\n+\n+ \t #if $advanced_hmm_params.set_hmm_params == "set":\n+ \t#if $advanced_hmm_params.threshold_params.clustering_threshold == "part":\n+ \t-a $advanced_hmm_params.threshold_params.part_threshold\n+ \t#end if\n+\n+ \t#if $advanced_hmm_params.threshold_params.clustering_threshold == "size":\n+ \t-s $advanced_hmm_params.threshold_params.size_threshold\n+ \t#end if\n+\n+ \t#if $advanced_hmm_params.threshold_params.clustering_threshold == "count":\n+ \t-c $advanced_hmm_params.threshold_params.count_threshold\n+ \t#end if\n+\t\t#if $advanced_hmm_params.unique == "unique":\n+\t\t\t--unique\n+\t\t#end if\n+\n+\t \t#set $n_field=""\n+\t \t#set $v_field=""\n+\t \t#set $r_field=""\n+\t\n+ \t \t#if $advanced_hmm_params.score_params.set_scores == "set":\n+\t\t\t#if $advanced_hmm_params.score_params.relative_scores == "relative":\n+ \t\t-e\n+ \t\t#end if\n+ \t\t#if $advanced_hmm_params.score_params.relative_scores == "absolute":\n+ \t\t-b\n+ \t\t#end if\n+\n+ \t#for $s in $advanced_hmm_params.score_params.round:\n+\t\t\t\t#set $n_field = $n_field + str($s.assign_score) + ","\n+\t\t\t\t#set $v_field = $v_field + str($s.overlap_score) + ","\n+\t\t\t\t#set $r_field = $r_field + str($s.merge_score) + ","\n+\t\t\t#end for\n+\n+\t\t\t-n $n_field\n+\t\t\t-v $v_field\n+\t\t\t-r $r_field\n+ \t#end if\n+\t \t#set $l_field=""\n+\n+ \t#if $advanced_hmm_params.match_state_params.set_max_aln_length == "set":\n+ \t-j $advanced_hmm_params.match_state_params.max_aln_length\n+ \t#end if\n+\n+ \t#if $advanced_hmm_params.extension_increase_length == "Yes":\n+ \t-q\n+ \t#end if\n+\n+\t\t-k $advanced_hmm_params.min_ic \n+\t\t-y $advanced_hmm_params.max_gap_proportion\n+\t\t-u $advanced_hmm_params.max_inner_gaps\n+\t\t-h $advanced_hmm_params.min_match_states\n+\t\t-C $advanced_hmm_params.min_correlation\n+\t#end if\t\t\n+\t\t\t\n+</command>\n+\n+ <inputs>\n+ <param format="fasta" name="input" type="data" label="Source sequence file" help="File with sequences to cluster in fasta format. See -i, --input in the manual for details." />\n+\n+<conditional name="label_params">\n+ <param name="set_labels" type="select" label="Specify a subset of labels to be used" help="Set Automatic to use all labels present in the data or choose a subset of labels to be used. See -l, --labels in the manual for details.">\n+ <option value="auto">Automatic - all labels</option>\n+ <option value="set">Set list of labels manually</option>\n+ </param>\n+ <when value="auto" />\n+ '..b'package" version="3.1b2">hmmer</requirement>\n+\t\t<requirement type="package" version="2.0.16">hhsuite</requirement>\n+ </requirements>\n+\n+\n+<tests>\n+ \t<test>\n+\t\t<param name="input" value="input.fa" />\n+\t\t<param name="advanced_initial_params.max_shift" value="3" />\n+\t\t<param name="advanced_initial_params.shift_penalty" value="0" />\n+\t\t<param name="advanced_initial_params.scoring_matrix" value="blosum62" />\n+\t\t<param name="advanced_hmm_params.min_match_states" value="4" />\n+\t\t<param name="advanced_hmm_params.min_ic " value="1.2" />\n+\t\t<param name="advanced_hmm_params.max_gap_proportion" value="0.05" />\n+\t\t<param name="advanced_hmm_params.max_inner_gaps" value="0" />\n+\n+\t\t<output name="output_clusters" file="output_clusters.csv" /> \n+\t\t<output name="output_sequences" file="output_sequences.csv" /> \n+\t</test>\n+</tests>\n+\n+\n+\n+<help>\n+\n+\n+**HAMMOCK version 1.1.0**\n+\n+**Hammock overview**\n+\n+Hammock performs peptide sequence clustering. It is able to identify clusters of sequences sharing a sequence motif within big datasets. For news, documentation and other available versions, see http://www.recamo.cz/en/software/hammock-cluster-peptides/\n+\n+------\n+\n+.. class:: infomark\n+\n+**Citation**\n+Please cite: \n+\n+Krejci, Adam, et al. "Hammock: a hidden Markov model-based peptide clustering algorithm to identify protein-interaction consensus motifs in large datasets." Bioinformatics 32.1 (2016): 9-16.\n+\n+------\n+\n+**Input format**\n+\n+Hammock accepts fasta files. For basic work, fasta description lines (those starting with ">") may contain virtually anything. For work with the concept of sequence labels, description line should be in this form: \n+\n+ | >id|count|label\n+\n+an example of two records in this format:\n+\n+ | >1|42|label1\n+ | RSPIVRQLPSLP\n+ | >2|58|label2\n+ | GSWVVDISNVED\n+\n+For more detailed description of the label concept and input format, see the documentation_.\n+\n+------\n+\n+**Outputs**\n+\n+Hammock returns three files, all of them are tab-separated tables.\n+\n+The first is the cluster overview file. It contains one line for each resulting cluster plus header. Columns are: \n+\n+cluster_id main_sequence sum label1 label2 label3 ...\n+\n+ | cluster_id: Cluster\'s unique numeric identifier.\n+ | main_sequence: The most popular (appearing in the highest number of copies) sequence of this cluster\n+ | sum: Total count of all sequences in this cluster (sum over all labels)\n+ | label1, label2 etc. Counts of sequences with particular labels\n+\n+\n+The second file provides more detailed information. It contains one line for each clustered (unique) sequence plus header. The sequences are ordered according to their presence in clusters, from the largest cluster and within a cluster, from the most abundant sequence.\n+\n+Columns are: \n+\n+cluster_id sequence alignment sum label1 label2 label3 ...\n+\n+ | cluster_id: Id of the cluster this sequence belongs to\n+ | sequence: Amino acid sequence of this peptide\n+ | alignment: Aligned amino acid sequence of this peptide (part of cluster\'s multiple sequence alignment)\n+ | sum: Total count of copies of this sequence (sum over all labels)\n+ | label1, label2 etc. Counts of copies with particular labels\n+\n+\n+The third file is the same as the second file, with two differences: it also contains sequences not belonging to any cluster (these have "NA" in the cluster_id column) and the order of the sequences in this file is the same as their order in the input fasta file.\n+\n+------\n+\n+**Parameters**\n+Default and auto-detected parameters have been carefully tuned and tested to work well with several datasets, they are especially suited for short peptides from phage display experiments. Neverheless, there is no such thing as universal rules suitable for every dataset - parameter understanding and tuning may be needed. For more detailed description of parameters, see the documentation_.\n+\n+.. _documentation: http://www.recamo.cz/userfiles/file/Software/Hammock/Hammock-manual.pdf\n+\n+\n+</help>\n+\n+</tool>\n' |
| b |
| diff -r 7950e4c52972 -r 22b245c1bb94 test-data/input.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/input.fa Fri Jun 23 06:33:16 2017 -0400 |
| b |
| b'@@ -0,0 +1,4914 @@\n+>5006\n+WVTAPRSLPVLP\n+>4863\n+GSWVVDISNVED\n+>4628\n+NYSGNRPLPGIW\n+>6642\n+RSPIVRQLPSLP\n+>5810\n+RALPVMPTNGPM\n+>4893\n+AKSRPLPMVGLV\n+>3919\n+VRPLPSPEGFGQ\n+>5831\n+YRGRMLPVIWGT\n+>4087\n+RALPLPRAYEGI\n+>6358\n+VPLLPIRNGAVN\n+>4358\n+PVRVLPNIPLSV\n+>6587\n+SYVPGVPLRNLA\n+>4003\n+TRVLPNLPVNSQ\n+>4836\n+PGLPSRSVSFFN\n+>3844\n+RGLPQRPWHSLL\n+>3889\n+LAQRPLPLVTAW\n+>5804\n+AGQARTLPAIVV\n+>5464\n+LAQRPLPLIAAW\n+>5401\n+ARASPQVPLGRI\n+>4319\n+VSAIIPELPPRG\n+>6327\n+RYIPSLPLRNLH\n+>4261\n+LRYRTFPNLPEL\n+>4429\n+RALPIPNLYMLV\n+>4066\n+ARALPQVPSGRI\n+>6375\n+KAKFIRELPTVP\n+>6631\n+RWVLPELPMNGV\n+>5215\n+RKLPTTPNVMSV\n+>5970\n+LGPRNRALPIIQ\n+>4094\n+RGLPGIPQGIKL\n+>6421\n+SGTWALPVPLFG\n+>4704\n+IRIHDRNLPVVP\n+>6578\n+RTLPVLPTNGPM\n+>5433\n+YVRYALPDLPVE\n+>4209\n+PPAVPLRGIDLL\n+>4784\n+RLRPLPLPMVTL\n+>6101\n+RPLPVFPSEVTE\n+>5554\n+WWRTPPPKVPFL\n+>4184\n+LVAPAIPFRAVE\n+>4676\n+RGLPDRPGLGVL\n+>3862\n+WTANLFRPLPFV\n+>4827\n+GMHLAHRALPLI\n+>4405\n+RPLPSIPGLYHV\n+>5671\n+ASNLGRLLPPVV\n+>5668\n+FRPLPAPAYSFG\n+>4304\n+RFYPLLPERNIV\n+>4180\n+RALPEVSALSHV\n+>4139\n+NYSPMVPALNEL\n+>5571\n+GLRALPSFPLGS\n+>4582\n+SSALPTRPLAFV\n+>5922\n+SGFTRALPSIPP\n+>6220\n+YSYKTRGLPAVP\n+>5105\n+IWDRQLLMVPVN\n+>5935\n+GPPAVPLRDIVV\n+>5097\n+LMIPALPDWNWN\n+>4422\n+RIAPHLPLMNTW\n+>6257\n+RALPEIGNHQTS\n+>3750\n+RFERPLPVVGEV\n+>5337\n+RSLPAIYLSGDM\n+>4649\n+LSVRGLPSIPTQ\n+>4873\n+FLATRTLPVPYL\n+>5745\n+GIPVVPPRNAVV\n+>6513\n+TVLLANRGLPLV\n+>6218\n+RPLPVIFNGFSG\n+>6207\n+LRYRTVLNLPEL\n+>6008\n+SFRGLPSIPWGT\n+>3641\n+LRYRELPVTTTV\n+>4128\n+LSDIWRIGPNLM\n+>5981\n+MRVSASDLPLLP\n+>4376\n+FGGNGNRPLPWL\n+>4243\n+RGLPSIPTQIFY\n+>4797\n+SLAPPLPGMNFV\n+>5238\n+LKHRELPFIALD\n+>6630\n+QSRALPILPVSD\n+>6335\n+VSWVTRKPPFLP\n+>4115\n+SVPDVPQRNVIW\n+>6048\n+ERWRALPDIPVQ\n+>6502\n+LANRALPTTILW\n+>4640\n+RQLPRVPLFSDV\n+>5225\n+RWWRPLPELASS\n+>6510\n+RPLPVISASGFI\n+>3648\n+WDRFTRASPLVP\n+>5748\n+SHSAMRWLPALL\n+>5578\n+GQTDRWLPAVPY\n+>5327\n+NVLGRLLPNPGM\n+>4342\n+RSLPGPPDAFPW\n+>3960\n+YRALPVFPTMSE\n+>5117\n+TLAPVVPARNGL\n+>3903\n+QVSQDLPPLPYT\n+>6290\n+SVWARGLPVSDL\n+>4849\n+GYSYGQLPATPW\n+>5592\n+WFSARMLPYLPA\n+>3738\n+RGPALPLRVLLR\n+>6381\n+AHLRALPMPLGA\n+>5625\n+KAKLIREMPTVP\n+>6239\n+YASVPPVRNQLE\n+>4933\n+TDGGRSLPEVPW\n+>3721\n+GPGLRGLPSIPV\n+>3935\n+VMNGRRLPLLPG\n+>5650\n+ARKLPRLPFTQD\n+>5224\n+SRSALPLWDVYD\n+>5129\n+MPLLPIRNGTVN\n+>4681\n+LHQQRALPMAQG\n+>4287\n+LMVRALPSIIMH\n+>5362\n+KGPLPMIPVRLL\n+>4481\n+VRPLPSPEVFGR\n+>4742\n+WRSLPAIPTSEF\n+>3969\n+GTRALPLVLERF\n+>4664\n+IQSRLLPVSPVE\n+>6113\n+RARQLPMVPFSQ\n+>5548\n+LWLGRTLTSVPS\n+>6024\n+ASRRLPSRPVAV\n+>4058\n+EGRSLPAVPEFK\n+>6085\n+GSQWWKRALPAP\n+>5488\n+RPLPRVPGSNAL\n+>4106\n+RKLPAVPATEFN\n+>6069\n+GNWTKDLPQIVI\n+>4176\n+SWVPYLPSRNQL\n+>5632\n+RGPLPPIGVDMS\n+>4560\n+RALPSAPYNAPY\n+>4076\n+SRALLTRPLAFV\n+>3832\n+PNWLRPLPGLRE\n+>4928\n+RALPVPPGGSVY\n+>6485\n+PVGRQLPMIRHI\n+>5150\n+LRALPAAPYGAL\n+>5077\n+PSSRALPGMPSI\n+>3779\n+VPLPLPNASGYG\n+>5724\n+SSRRLPLVPTYE\n+>3747\n+NEQLFHRPLPAV\n+>6060\n+ARPPLPGYNKAM\n+>5369\n+LRYRTVPNLPAL\n+>3880\n+WTGLQYRILPTG\n+>6468\n+GAIPRFLPPIPH\n+>4989\n+LRSLPSVPRFGN\n+>6192\n+VTWRALPDVPAG\n+>5417\n+LYRALPMVYADA\n+>6211\n+VPWRALPEVPAG\n+>5299\n+LPELPSANFDWN\n+>4978\n+LRRRLPAIVELD\n+>3775\n+RALPIAPDSIFY\n+>5690\n+SRALPTRPLAFA\n+>3780\n+GRSLPSLPMGLF\n+>4847\n+LHTALPPLPSSM\n+>5240\n+TRVSARDLPLLP\n+>4579\n+IQSRDLPMVHPY\n+>6074\n+FRALPRVPVYVL\n+>4783\n+VRKLPKRPTVVI\n+>5476\n+SGNTRPLPALSL\n+>4456\n+SVARAMMALPGV\n+>4132\n+VRVRALPAAPSI\n+>5152\n+AMIHERPLPIVG\n+>5564\n+LLMQRPLPWEPV\n+>5561\n+RTVMISRPLPFP\n+>4191\n+RVLPDVPSMQRS\n+>4945\n+TRPLPSVIDVSM\n+>3817\n+RKLPPTHNVMSV\n+>5354\n+RGLPDRPGLGGL\n+>3687\n+RWLPSLPHNVPF\n+>5450\n+FGPALPARWGGV\n+>4597\n+LRSLPSVPWLGN\n+>3839\n+QIPSLPLRNQDT\n+>6398\n+RLPLKRPLPSLP\n+>4590\n+VGRAFRMLPDVT\n+>5193\n+FGPRNRALPIIQ\n+>3761\n+HAWWRPWTGVLV\n+>6058\n+GSWVVDISNVEE\n+>6199\n+LSVRGLPNIPSQ\n+>3825\n+TVFPGRPLPTPH\n+>5976\n+YAPVPPVRNQLK\n+>6532\n+VGWSRALPALPS\n+>4500\n+VPLLPTRNGTVN\n+>5410\n+LWLGRTFPSVPS\n+>5301\n+LAMRALPLINLF\n+>4956\n+RPLPSVPSAVGL\n+>6458\n+LAVRALPLINLL\n+>6609\n+SYRALPYAPTVI\n+>5973\n+RALPLLPRLAGV\n+>5502\n+PPPLPARFRIWT\n+>4969\n+RPLPELPERNFL\n+>6529\n+VRSLPGVPVFHS\n+>4722\n+GVTLLLPARNLY\n+>4729\n+RRPLPGLGYMML\n+>4329\n+RDLPPFPDAYIV\n+>6077\n+GRGLPNIPDVGV\n+>4662\n+RARMALPMPYAL\n+>6033\n+GPILPPFNSIRQ\n+>6137\n+LRIRESPLIEVS\n+>3992\n+LMVPAIPDWNWN\n+>5856\n+ARSWAQLPTLPI\n+>4988\n+GQSGRSLPSVPF\n+>6098\n+GGW'..b'DIPLHGVL\n+>6161\n+PMRSLPDLPRVV\n+>4538\n+GPVLPQRNVAHN\n+>4062\n+VLGPPVPPQNVS\n+>6096\n+GVALRTRALPVI\n+>5712\n+VGVPLPARSLAL\n+>6600\n+YSSRIRPLPLVE\n+>6607\n+LGGRVLPIPMPV\n+>4267\n+WGNGPLPVIPRL\n+>3715\n+PGQWAPNLPERY\n+>5055\n+GPIVPFRYVLWV\n+>5545\n+LGDRPLPSVIGV\n+>5277\n+AGPRLPARADVV\n+>4754\n+SYRALPVISEAD\n+>4679\n+LQYRELPVTTTM\n+>5395\n+PGLPGRNIVLIP\n+>4472\n+WPGARRLPGLSW\n+>4762\n+SHSAMRRLPALW\n+>5574\n+LQGRYISLPEIP\n+>4769\n+QALPSLPVRYGA\n+>5445\n+RALPRIPLQADI\n+>4111\n+LGARGLPTIPFH\n+>4903\n+DLRPRLPARWGI\n+>4118\n+MERALPAVPVDL\n+>5272\n+RPLPMIGKTWEI\n+>5486\n+RPLPVLEPSEYN\n+>5580\n+LRVSSLPVIQML\n+>4572\n+FGRALPVLPVVT\n+>4546\n+NWNSSRPLPALV\n+>5951\n+LRLRSLPVIQML\n+>5316\n+QYRALPSAPGYI\n+>5739\n+SGLIRWLPTIPG\n+>4958\n+VSFLYRRLPMVY\n+>5319\n+SMRSLPDLQRVV\n+>5543\n+RFERPLPVVGEG\n+>5153\n+LPDLPARTHSGF\n+>4917\n+LWRRTSLPSLPV\n+>4338\n+LSVLGLPNIPTQ\n+>5366\n+TYSGSQRALPVV\n+>3830\n+GGPMVPPRFLIL\n+>6065\n+GPIVPFRDVYVL\n+>4612\n+LRYRAVPNLPEL\n+>4170\n+KAGLRELPAVVS\n+>4017\n+GQISRLPPVLPD\n+>6483\n+YDRALPNTPGLD\n+>5269\n+VPWRALPDAPAG\n+>5253\n+AVFRMLPALPSW\n+>3795\n+YVYYYAGLPVVP\n+>4913\n+RPVPMPPSFDIT\n+>5484\n+ATFGWYALAMEW\n+>3770\n+SESRALPEIPYL\n+>3725\n+TRRLPGVPQVLL\n+>4174\n+FGRSNVLLPAVP\n+>6386\n+RSLPKLPGWYSV\n+>4785\n+RAGPMLPDRNLH\n+>5357\n+AVGPAVDIRWLV\n+>5888\n+RKLPPTPNVMSI\n+>5053\n+FSVRGLPNIPTQ\n+>6197\n+GPVVPYRFLAGF\n+>5566\n+GLGQRTLSIIPV\n+>6554\n+LPRLPMRVLRAG\n+>5978\n+FGRPLPPIVYGQ\n+>5197\n+RKLPHTPNVMSV\n+>3872\n+RVTSRALPILDV\n+>6537\n+YRWRGLPIIAGV\n+>3964\n+SRALSWRILPVV\n+>5529\n+NRHLPKLPVLVT\n+>4378\n+KAKLIRELPTVS\n+>5729\n+GPALPARWSLNM\n+>5624\n+WWRFFSVDEAIV\n+>5007\n+WLNVLRNLPIVP\n+>4452\n+NRWRPLPVPHAL\n+>5456\n+TRWRILPEVPAS\n+>5585\n+RVGRALPDILLS\n+>3749\n+VLRPELPSRNMV\n+>4469\n+PSSRALPGTPSI\n+>6443\n+GQLVLPSIPVDL\n+>6277\n+GLRSLPFPPSAL\n+>6258\n+GGWRDSALPFTP\n+>4563\n+VVNGRRLPLLPG\n+>5472\n+RALPVPPGDSVY\n+>5264\n+LRYREPPVTTTI\n+>3860\n+GQTDRWLSAVPY\n+>5307\n+SFFGRTLPVIGS\n+>4260\n+VSRALPAMPYGM\n+>6362\n+LSDLPARTHSGF\n+>4240\n+VRELPRLPLGSL\n+>4636\n+RAPLPPVPVLAS\n+>3997\n+FGPLSMAPGYAV\n+>4592\n+RPLPVPLTDLSL\n+>4922\n+SFFGRTLPVIGG\n+>4459\n+VYGRALPMAPYR\n+>5820\n+TNRDLPSLPDTF\n+>4275\n+LFRSRLPMVPYA\n+>5693\n+VYGRALPTAPYQ\n+>4175\n+RPELPARNQMAV\n+>6018\n+RALPVLPTYGPM\n+>4055\n+AAMRDLPAWPVS\n+>4807\n+FPQLPARYSANV\n+>4136\n+RGPLPVTPGYGL\n+>5151\n+LHQQRALPMVQG\n+>3801\n+PRFRMLPAVLRV\n+>4986\n+PSARPLPQYPSY\n+>5634\n+RELPFPPVAVVQ\n+>5434\n+RPLPLIDRTFGL\n+>5026\n+SPPPLPSRGMSI\n+>6613\n+RPLPVIAAYNQV\n+>5975\n+APRVPMRGYEVN\n+>6499\n+HGRSLPARPLLY\n+>4677\n+SQVVRALPVVNL\n+>6426\n+RGALPSLPGGLY\n+>6083\n+RRLPEPGLIAGT\n+>3907\n+RALPVPPSDSVY\n+>5771\n+LMVPALPDWNWK\n+>6524\n+VPSLPIRNGTVN\n+>4974\n+RHNGLPQVPGFL\n+>5651\n+QVSRDLSPLPYT\n+>3691\n+TVPELPERMQIT\n+>5673\n+AYRFLPAVPGDQ\n+>3650\n+RRTLPDWPLSVY\n+>6279\n+VPLLLIRNGTVN\n+>4182\n+RSFAPLPLTPHE\n+>5461\n+LSRPLPGLPQTL\n+>6034\n+PPNLPYRMIKSM\n+>5881\n+WRNDSRPLPAIS\n+>4265\n+LWLGRTLPSVPR\n+>5219\n+VVTGPILPSRLV\n+>6318\n+GIRSLPALPGLN\n+>6455\n+VATFGPLPSPWT\n+>4039\n+RVLPVLPSANQW\n+>3703\n+RRSLPIIPINGD\n+>5714\n+YYNRRLPDLRVF\n+>5778\n+GVGLFRFLPPAP\n+>4879\n+RALPPVPLTQIK\n+>4894\n+RLELPVRNIMYD\n+>5479\n+PRGLLPVAPGWA\n+>4697\n+IRPLPPAYNEHI\n+>4125\n+ARSAYRILPSIV\n+>4559\n+QVSRGLPPLPYT\n+>4765\n+KKRPLPAIEHFH\n+>3952\n+GQQVLPSIPVDL\n+>4371\n+LAVRSLPLINLF\n+>4905\n+RLVTYRALPLIM\n+>5332\n+RAPELPDRIYVV\n+>6296\n+RFDRPLPVVGDV\n+>5897\n+RRLPLIPGEMLI\n+>4711\n+SRALPTRPLVFV\n+>4645\n+SRPTLPARLYYY\n+>4404\n+DGAPPLPVWNVV\n+>6562\n+GLNVLRNLPFVP\n+>3645\n+PPGLPQRSFVAG\n+>5602\n+PSERPLPHVPSQ\n+>4306\n+TNRLLPNVPGFV\n+>6224\n+MRALPVLDVISQ\n+>5098\n+RLLPGIPTAMAM\n+>4123\n+NRTLPSVPTSNF\n+>3959\n+YAGLAYRALPSV\n+>6047\n+GRSLPMLPADTR\n+>5210\n+RWLPEIPVNMSN\n+>3942\n+WRVPSALPPVPI\n+>6448\n+DLYAPRGLPLPP\n+>6409\n+LSRRLPSILTVQ\n+>5746\n+AALAPATPRRAL\n+>6583\n+STRPLPALNQMD\n+>6370\n+FRRGLPIISSVV\n+>6270\n+WSLGGRSLPSLP\n+>6102\n+LSVRGLPNIPNQ\n+>4700\n+GTANLSRPLPFV\n+>4720\n+LMVKALPSIIMQ\n+>5926\n+GPRMLPALPTLV\n+>3753\n+LRSLPSAPWFGN\n+>3894\n+WARRGLPEIPLT\n+>4583\n+AAMRDLPARPVS\n+>6231\n+PVLSGRNIVLIP\n+>6368\n+RLELPARNIMYD\n+>4727\n+VRTILDSGLYKS\n+>5076\n+GRPLLPVRNLGM\n+>4064\n+LPQVPLRNLGAN\n+>4162\n+HRWRPLTVPHAL\n+>4045\n+MHTRPLPAILFG\n+>3922\n+RGLGRALPIVPG\n+>5893\n+QRSLPSVPNHTL\n+>4746\n+RFSGRPLPMPFQ\n+>4877\n+RALWRVLPVEPL\n+>5497\n+VPKVPPRFANYL\n+>4825\n+PMSLPTVDMTQW\n+>6576\n+GAPTLPVRNLLY\n+>4197\n+GYRPLPGIPDTE\n+>6053\n+NNLYKFRELPVV\n+>4366\n+WRSLPAIPTYEL\n+>3869\n+VRWRMLPATLGV\n' |
| b |
| diff -r 7950e4c52972 -r 22b245c1bb94 test-data/output_clusters.csv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/output_clusters.csv Fri Jun 23 06:33:16 2017 -0400 |
| b |
| @@ -0,0 +1,3 @@ +cluster_id;main_sequence;sum;no_label +43;AAMFLRPLPAVQ;1738;1738 +51;AALAPATPRRAL;415;415 |
| b |
| diff -r 7950e4c52972 -r 22b245c1bb94 test-data/output_sequences.csv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/output_sequences.csv Fri Jun 23 06:33:16 2017 -0400 |
| b |
| b'@@ -0,0 +1,2154 @@\n+cluster_id;sequence;alignment;sum;no_label\n+43;YYYKTRGLPAVP;-YYYKTRGLPAVP------;1;1\n+43;YYNRRLPDLRVF;---YYNRRLPDLRVF----;1;1\n+43;YWPDLPAVPYDQ;----YWPDLPAVPYDQ---;1;1\n+43;YVYYYAGLPVVP;-YVYYYAGLPVVP------;1;1\n+43;YVRYALPDLPVE;---YVRYALPDLPVE----;1;1\n+43;YVRVLPNIPMTK;----YVRVLPNIPMTK---;1;1\n+43;YVALGHRDLPQL;YVALGHRDLPQL-------;1;1\n+43;YTTLSLPSLPNA;---YTTLSLPSLPNA----;1;1\n+43;YTARVLPGIYEF;---YTARVLPGIYEF----;1;1\n+43;YSYKTRGLPAVP;-YSYKTRGLPAVP------;1;1\n+43;YSVRMLPQVPNS;---YSVRMLPQVPNS----;1;1\n+43;YSSRIRPLPLVE;-YSSRIRPLPLVE------;1;1\n+43;YSRPLPFPHSWV;----YSRPLPFPHSWV---;1;1\n+43;YSQRVRALPMFP;-YSQRVRALPMFP------;1;1\n+43;YSQRALPGVSDV;---YSQRALPGVSDV----;1;1\n+43;YSLKGLPLLPRL;---YSLKGLPLLPRL----;1;1\n+43;YSLGRALPSPIL;--YSLGRALPSPIL-----;1;1\n+43;YSGLANRALPSV;YSGLANRALPSV-------;1;1\n+43;YSDRPLPIPAVI;-YSDRPLPIPAVI------;1;1\n+43;YSARTLPGIFHV;---YSARTLPGIFHV----;1;1\n+43;YRWRPLPVPHAL;---YRWRPLPVPHAL----;1;1\n+43;YRWRMLPVIWGT;---YRWRMLPVIWGT----;1;1\n+43;YRWRGLPIIAGV;---YRWRGLPIIAGV----;1;1\n+43;YRWRFLPSLDAL;---YRWRFLPSLDAL----;1;1\n+43;YRWRALPSVSTD;---YRWRALPSVSTD----;1;1\n+43;YRVLPTLPYNMT;-----YRVLPTLPYNMT--;1;1\n+43;YRRPLPSFVQSI;----YRRPLPSFVQSI---;1;1\n+43;YRRELPVIFYEV;----YRRELPVIFYEV---;1;1\n+43;YRPLPTVPRYIE;-----YRPLPTVPRYIE--;1;1\n+43;YRGRMLPVIWGT;---YRGRMLPVIWGT----;1;1\n+43;YRALPVFPTMSE;-----YRALPVFPTMSE--;1;1\n+43;YQSRALPAVWSW;---YQSRALPAVWSW----;1;1\n+43;YNRNLGRELPIL;YNRNLGRELPIL-------;1;1\n+43;YMNWGRALPHPS;-YMNWGRALPHPS------;1;1\n+43;YMFKDVQLPVVP;-YMFKDVQLPVVP------;1;1\n+43;YLPLPGLPFGLV;-----YLPLPGLPFGLV--;1;1\n+43;YLLGFRPLPMVS;-YLLGFRPLPMVS------;1;1\n+43;YLFRALPDVPRN;---YLFRALPDVPRN----;1;1\n+43;YGTRTLPRVILD;---YGTRTLPRVILD----;1;1\n+43;YGRALSGLPSLP;-YGRALSGLPSLP------;1;1\n+43;YGQRPLPLVDGW;---YGQRPLPLVDGW----;1;1\n+43;YGPLPRIPIGYD;-----YGPLPRIPIGYD--;1;1\n+43;YGNPRARMLPII;YGNPRARMLPII-------;1;1\n+43;YGHPTLPAIPVL;---YGHPTLPAIPVL----;1;1\n+43;YGGRLLPLVPVF;---YGGRLLPLVPVF----;1;1\n+43;YGGRLLPLVPGF;---YGGRLLPLVPGF----;1;1\n+43;YGGRLLPDRPNF;---YGGRLLPDRPNF----;1;1\n+43;YGDLAHRALPAV;YGDLAHRALPAV-------;1;1\n+43;YGAGRLLPPLPW;--YGAGRLLPPLPW-----;1;1\n+43;YDRALPNTPGLD;----YDRALPNTPGLD---;1;1\n+43;YDGRFRTLPIPV;-YDGRFRTLPIPV------;1;1\n+43;YARYALPDLPVE;---YARYALPDLPVE----;1;1\n+43;YAIYKLGLPDVP;-YAIYKLGLPDVP------;1;1\n+43;YAGPANRALPSV;YAGPANRALPSV-------;1;1\n+43;YAGMANRALPSV;YAGMANRALPSV-------;1;1\n+43;YAGLAYRALPSV;YAGLAYRALPSV-------;1;1\n+43;YAGLANRALPSV;YAGLANRALPSV-------;1;1\n+43;YAELANRALPSV;YAELANRALPSV-------;1;1\n+43;WYHGLPAVPMYN;----WYHGLPAVPMYN---;1;1\n+43;WWSNRALPMLMV;--WWSNRALPMLMV-----;1;1\n+43;WWRTPLPKVPFM;---WWRTPLPKVPFM----;1;1\n+43;WWRTPLPKVPFL;---WWRTPLPKVPFL----;1;1\n+43;WVVRPLPVVGAF;---WVVRPLPVVGAF----;1;1\n+43;WVTAPRSLPVLP;-WVTAPRSLPVLP------;1;1\n+43;WVRWKELPMVPH;--WVRWKELPMVPH-----;1;1\n+43;WVRPLPELYMIG;----WVRPLPELYMIG---;1;1\n+43;WVRPLPELHMIG;----WVRPLPELHMIG---;1;1\n+43;WVMAPRSLPVLP;-WVMAPRSLPVLP------;1;1\n+43;WVHQLRPLPLPV;-WVHQLRPLPLPV------;1;1\n+43;WVGWKELPMVPH;--WVGWKELPMVPH-----;1;1\n+43;WTVMGRALPVLG;-WTVMGRALPVLG------;1;1\n+43;WTSRTLPSVPFF;---WTSRTLPSVPFF----;1;1\n+43;WTGLRYRILPTV;WTGLRYRILPTV-------;1;1\n+43;WTGLQYRILPTV;WTGLQYRILPTV-------;1;1\n+43;WTGLQYRILPTI;WTGLQYRILPTI-------;1;1\n+43;WTGLQYRILPTG;WTGLQYRILPTG-------;1;1\n+43;WTAVWRSLPIIP;-WTAVWRSLPIIP------;1;1\n+43;WTAVGRSLPVIP;-WTAVGRSLPVIP------;1;1\n+43;WTAVGRSLPIIP;-WTAVGRSLPIIP------;1;1\n+43;WTAVGRSLHIIP;-WTAVGRSLHIIP------;1;1\n+43;WTANLFRPLPFV;WTANLFRPLPFV-------;1;1\n+43;WSYPSRALPRVP;-WSYPSRALPRVP------;1;1\n+43;WSWRALPELWFD;---WSWRALPELWFD----;1;1\n+43;WSSLPAIPTYEF;-----WSSLPAIPTYEF--;1;1\n+43;WSRALPRVPMTD;----WSRALPRVPMTD---;1;1\n+43;WSRALPIIGAGT;----WSRALPIIGAGT---;1;1\n+43;WSQRSLPDIVAY;---WSQRSLPDIVAY----;1;1\n+43;WSLRRALPVEPF;--WSLRRALPVEPF-----;1;1\n+43;WSLHRALPVEPF;--WSLHRALPVEPF-----;1;1\n+43;WSLGGRSLPSLP;-WSLGGRSLPSLP------;1;1\n+43;WSKPMRPLPVML;-WSKPMRPLPVML------;1;1\n+43;WRYLPSPPESAL;-----WRYLPSPPESAL--;1;1\n+43;WRWRALPFVDIA;---WRWRALPFVDIA----;1;1\n+43;WRVPSALPSIPI;--WRVPSALPSIPI-----;1;1\n+43;WRVPSALPPVPI;--WRVPSALPPVPI-----;1;1\n+43;WRVPSALPPIPI;--WRVPSALPPIPI-----;1;1\n'..b'51;GPPAVPLRDIVV;----GPPAVPLRDIVV--;1;1\n+51;GPMLPVWNSVGS;-----GPMLPVWNSVGS-;1;1\n+51;GPLLPVRSVDLL;-----GPLLPVRSVDLL-;1;1\n+51;GPLLPVRSADLL;-----GPLLPVRSADLL-;1;1\n+51;GPLLPPRMAMLK;-----GPLLPPRMAMLK-;1;1\n+51;GPIVPFRYVLWV;-----GPIVPFRYVLWV-;1;1\n+51;GPIVPFRNVYVL;-----GPIVPFRNVYVL-;1;1\n+51;GPIVPFRDVYVL;-----GPIVPFRDVYVL-;1;1\n+51;GPILPPFNSIRQ;-----GPILPPFNSIRQ-;1;1\n+51;GPILPPFNSIGQ;-----GPILPPFNSIGQ-;1;1\n+51;GPILPKREWVSV;-----GPILPKREWVSV-;1;1\n+51;GPFLPVRNSSIW;-----GPFLPVRNSSIW-;1;1\n+51;GPFLPERNVVAV;-----GPFLPERNVVAV-;1;1\n+51;GPELPSRTVYTD;-----GPELPSRTVYTD-;1;1\n+51;GPDVPKRSYIES;-----GPDVPKRSYIES-;1;1\n+51;GPDLPPWVLNLV;-----GPDLPPWVLNLV-;1;1\n+51;GPALPFRVWSDL;-----GPALPFRVWSDL-;1;1\n+51;GPALPFRNSIYV;-----GPALPFRNSIYV-;1;1\n+51;GPALPFRNSIYA;-----GPALPFRNSIYA-;1;1\n+51;GPALPARWSSNM;-----GPALPARWSSNM-;1;1\n+51;GPALPARWSLNM;-----GPALPARWSLNM-;1;1\n+51;GPALPARWSFNM;-----GPALPARWSFNM-;1;1\n+51;GPALPARTVGIL;-----GPALPARTVGIL-;1;1\n+51;GLVLPQRNVAHN;-----GLVLPQRNVAHN-;1;1\n+51;GLQPVLPPRNLV;---GLQPVLPPRNLV---;1;1\n+51;GLQPGLPPRNLV;---GLQPGLPPRNLV---;1;1\n+51;GLPAVPLRDIVV;----GLPAVPLRDIVV--;1;1\n+51;GLELPARNIMYD;-----GLELPARNIMYD-;1;1\n+51;GKPGLPLRPVVL;----GKPGLPLRPVVL--;1;1\n+51;GIPVVPPRNAVV;----GIPVVPPRNAVV--;1;1\n+51;GIPEIPARNWAV;----GIPEIPARNWAV--;1;1\n+51;GIPEIPAGNWAV;----GIPEIPAGNWAV--;1;1\n+51;GGSPELPKRNVW;---GGSPELPKRNVW---;1;1\n+51;GGPMVPPRFWIL;----GGPMVPPRFWIL--;1;1\n+51;GGPMVPPRFLIL;----GGPMVPPRFLIL--;1;1\n+51;GDKPMVPARAFL;---GDKPMVPARAFL---;1;1\n+51;GAPTLPVRNLLY;----GAPTLPVRNLLY--;1;1\n+51;GAPALPDRVSAF;----GAPALPDRVSAF--;1;1\n+51;FVPPLPARNNFI;----FVPPLPARNNFI--;1;1\n+51;FSPSLPIRNAYM;----FSPSLPIRNAYM--;1;1\n+51;FSAPALPARSDW;---FSAPALPARSDW---;1;1\n+51;FRPLLPPRLEGL;----FRPLLPPRLEGL--;1;1\n+51;FRPLLPPRLEEL;----FRPLLPPRLEEL--;1;1\n+51;FPVVPPRNLMGL;-----FPVVPPRNLMGL-;1;1\n+51;FPQLPARYSANV;-----FPQLPARYSANV-;1;1\n+51;FPQLPARYSAIV;-----FPQLPARYSAIV-;1;1\n+51;FPPVPYRSELTL;-----FPPVPYRSELTL-;1;1\n+51;FPILPSRTMAAV;-----FPILPSRTMAAV-;1;1\n+51;FPALPSLNSVFD;-----FPALPSLNSVFD-;1;1\n+51;FMPPLVPARVAL;---FMPPLVPARVAL---;1;1\n+51;FLPWSLPARNSY;---FLPWSLPARNSY---;1;1\n+51;FKGPQLPMANAW;---FKGPQLPMANAW---;1;1\n+51;FGSPRLPPRNLA;---FGSPRLPPRNLA---;1;1\n+51;FGSPRLPPRDLA;---FGSPRLPPRDLA---;1;1\n+51;FGPALPARWGGV;----FGPALPARWGGV--;1;1\n+51;FGGPMLPSWNVF;---FGGPMLPSWNVF---;1;1\n+51;FGGPILPSWNVF;---FGGPILPSWNVF---;1;1\n+51;FAPVLPERNPTM;----FAPVLPERNPTM--;1;1\n+51;EYSPSLPVWNLT;---EYSPSLPVWNLT---;1;1\n+51;EYPNLPARNVYL;----EYPNLPARNVYL--;1;1\n+51;EYGPTLPYRVLL;---EYGPTLPYRVLL---;1;1\n+51;ERPLLPVRNLGI;----ERPLLPVRNLGI--;1;1\n+51;ELSPPVPTRYYM;---ELSPPVPTRYYM---;1;1\n+51;DVAPALPVRLAV;---DVAPALPVRLAV---;1;1\n+51;DLRPRLPARWVI;---DLRPRLPARWVI---;1;1\n+51;DLRPRLPARWMI;---DLRPRLPARWMI---;1;1\n+51;DLRPRLPARWGI;---DLRPRLPARWGI---;1;1\n+51;DLGPLLPSRNVS;---DLGPLLPSRNVS---;1;1\n+51;DLAPLLPSRNVS;---DLAPLLPSRNVS---;1;1\n+51;DGPKLPPWNVSL;----DGPKLPPWNVSL--;1;1\n+51;DGAPSLPVWNVV;---DGAPSLPVWNVV---;1;1\n+51;DGAPPLPVWNVV;---DGAPPLPVWNVV---;1;1\n+51;AYPPYLPSRFLL;---AYPPYLPSRFLL---;1;1\n+51;AVPTIPQRNYVL;----AVPTIPQRNYVL--;1;1\n+51;ARPPLPGYNKAM;----ARPPLPGYNKAM--;1;1\n+51;ARLPARNAAYLV;------ARLPARNAAYLV;1;1\n+51;APVLPFREQLLL;-----APVLPFREQLLL-;1;1\n+51;APVLPARIWYDV;-----APVLPARIWYDV-;1;1\n+51;APTLPARMYVGS;-----APTLPARMYVGS-;1;1\n+51;APRVPMRGYEVN;-----APRVPMRGYEVN-;1;1\n+51;APRLPGRSLAMV;-----APRLPGRSLAMV-;1;1\n+51;APLLPYRIGEHW;-----APLLPYRIGEHW-;1;1\n+51;APLLPIRNGTVN;-----APLLPIRNGTVN-;1;1\n+51;APKLPVRGVTSF;-----APKLPVRGVTSF-;1;1\n+51;APIVPARVMALA;-----APIVPARVMALA-;1;1\n+51;APIAPLRNGMGF;-----APIAPLRNGMGF-;1;1\n+51;APALPTRFLRDL;-----APALPTRFLRDL-;1;1\n+51;APALPMRSYVDW;-----APALPMRSYVDW-;1;1\n+51;APALPLRNDGRY;-----APALPLRNDGRY-;1;1\n+51;APAFPSRNIVLK;-----APAFPSRNIVLK-;1;1\n+51;ALVDVAPPLPVR;ALVDVAPPLPVR------;1;1\n+51;ALLVPSLPPWLW;--ALLVPSLPPWLW----;1;1\n+51;AIMPEVPQRNWV;---AIMPEVPQRNWV---;1;1\n+51;AGYAPAVPIWYM;--AGYAPAVPIWYM----;1;1\n+51;AGPRLPARADVV;----AGPRLPARADVV--;1;1\n+51;AGLPLVPLRNLL;---AGLPLVPLRNLL---;1;1\n+51;AGLPLVPLRNLI;---AGLPLVPLRNLI---;1;1\n+51;AFAGPPILPARI;-AFAGPPILPARI-----;1;1\n+51;AALPKLPFRNMT;---AALPKLPFRNMT---;1;1\n+51;AALAPATPRRAL;--AALAPATPRRAL----;1;1\n' |
| b |
| diff -r 7950e4c52972 -r 22b245c1bb94 tool_dependencies.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_dependencies.xml Fri Jun 23 06:33:16 2017 -0400 |
| b |
| @@ -0,0 +1,116 @@ +<?xml version="1.0"?> +<tool_dependency> + <package name="clustalomega" version="1.2.0"> + <install version="1.0"> + <actions_group> + <actions architecture="x86_64" os="linux"> + <action type="download_by_url">http://www.clustal.org/omega/clustalo-1.2.0-Ubuntu-x86_64</action> + <action type="shell_command">chmod 755 clustalo-1.2.0-Ubuntu-x86_64</action> + <action type="move_file"> + <source>clustalo-1.2.0-Ubuntu-x86_64</source> + <destination>$INSTALL_DIR</destination> + </action> + <action type="shell_command">sed -i "s%#clustalOmegaCommand=%clustalOmegaCommand=$INSTALL_DIR/clustalo-1.2.0-Ubuntu-x86_64%g" $REPOSITORY_INSTALL_DIR/Hammock/settings/settings.prop</action> + </actions> + <actions architecture="x86_64" os="darwin"> + <action type="download_by_url">http://www.clustal.org/omega/clustal-omega-1.2.0-macosx</action> + <action type="shell_command">chmod 755 clustalo-1.2.0-Ubuntu-x86_64</action> + <action type="move_file"> + <source>clustalo-1.2.0-Ubuntu-x86_64</source> + <destination>$INSTALL_DIR</destination> + </action> + <action type="shell_command">sed -i "s%#clustalOmegaCommand=%clustalOmegaCommand=$INSTALL_DIR/clustalo-1.2.0-Ubuntu-x86_64%g" $REPOSITORY_INSTALL_DIR/Hammock/settings/settings.prop</action> + </actions> + </actions_group> + </install> + </package> + + <package name="hmmer" version="3.1b2"> + <install version="1.0"> + <actions_group> + <actions architecture="x86_64" os="linux"> + <action type="download_by_url">http://eddylab.org/software/hmmer3/3.1b2/hmmer-3.1b2-linux-intel-x86_64.tar.gz</action> + <action type="move_file"> + <source>binaries/hmmbuild</source> + <destination>$INSTALL_DIR</destination> + </action> + <action type="move_file"> + <source>binaries/hmmsearch</source> + <destination>$INSTALL_DIR</destination> + </action> + <action type="shell_command">sed -i "s%#hmmbuildCommand=%hmmbuildCommand=$INSTALL_DIR/hmmbuild%g" $REPOSITORY_INSTALL_DIR/Hammock/settings/settings.prop</action> + <action type="shell_command">sed -i "s%#hmmsearchCommand=%hmmsearchCommand=$INSTALL_DIR/hmmsearch%g" $REPOSITORY_INSTALL_DIR/Hammock/settings/settings.prop</action> + </actions> + <actions architecture="x86_64" os="darwin"> + <action type="download_by_url">http://selab.janelia.org/software/hmmer3/3.1b1/hmmer-3.1b1-macosx-intel.tar.gz</action> + <action type="move_file"> + <source>binaries/hmmbuild</source> + <destination>$INSTALL_DIR</destination> + </action> + <action type="move_file"> + <source>binaries/hmmsearch</source> + <destination>$INSTALL_DIR</destination> + </action> + <action type="shell_command">sed -i "s%#hmmbuildCommand=%hmmbuildCommand=$INSTALL_DIR/hmmbuild%g" $REPOSITORY_INSTALL_DIR/Hammock/settings/settings.prop</action> + <action type="shell_command">sed -i "s%#hmmsearchCommand=%hmmsearchCommand=$INSTALL_DIR/hmmsearch%g" $REPOSITORY_INSTALL_DIR/Hammock/settings/settings.prop</action> + </actions> + </actions_group> + </install> + </package> + + <package name="hhsuite" version="2.0.16"> + <install version="1.0"> + <actions_group> + <actions architecture="x86_64" os="linux"> + <action type="download_by_url">http://wwwuser.gwdg.de/~compbiol/data/hhsuite/releases/all/hhsuite-2.0.16-linux-x86_64.tar.gz</action> + <action type="move_file"> + <source>bin/hhmake</source> + <destination>$INSTALL_DIR</destination> + </action> + <action type="move_file"> + <source>bin/hhsearch</source> + <destination>$INSTALL_DIR</destination> + </action> + <action type="move_file"> + <source>lib</source> + <destination>$INSTALL_DIR</destination> + </action> + <action type="shell_command">sed -i "s%#hhmakeCommand=%hhmakeCommand=$INSTALL_DIR/hhmake%g" $REPOSITORY_INSTALL_DIR/Hammock/settings/settings.prop</action> + <action type="shell_command">sed -i "s%#hhsearchCommand=%hhsearchCommand=$INSTALL_DIR/hhsearch%g" $REPOSITORY_INSTALL_DIR/Hammock/settings/settings.prop</action> + <action type="shell_command">sed -i "s%#reformatCommand=%reformatCommand=$INSTALL_DIR/lib/hh/scripts/reformat.pl%g" $REPOSITORY_INSTALL_DIR/Hammock/settings/settings.prop</action> + <action type="set_environment"> + <environment_variable name="HHLIB" action="set_to">$INSTALL_DIR/lib/hh</environment_variable> + </action> + </actions> + <actions architecture="x86_64" os="darwin"> + <action type="download_by_url">ftp://toolkit.genzentrum.lmu.de/pub/HH-suite/releases/hhsuite-2.0.16-macosx.tar.gz</action> + <action type="move_file"> + <source>bin/hhmake</source> + <destination>$INSTALL_DIR</destination> + </action> + <action type="move_file"> + <source>bin/hhsearch</source> + <destination>$INSTALL_DIR</destination> + </action> + <action type="move_file"> + <source>lib</source> + <destination>$INSTALL_DIR</destination> + </action> + <action type="shell_command">sed -i "s%#hhmakeCommand=%hhmakeCommand=$INSTALL_DIR/hhmake%g" $REPOSITORY_INSTALL_DIR/Hammock/settings/settings.prop</action> + <action type="shell_command">sed -i "s%#hhsearchCommand=%hhsearchCommand=$INSTALL_DIR/hhsearch%g" $REPOSITORY_INSTALL_DIR/Hammock/settings/settings.prop</action> + <action type="shell_command">sed -i "s%#reformatCommand=%reformatCommand=$INSTALL_DIR/lib/hh/scripts/reformat.pl%g" $REPOSITORY_INSTALL_DIR/Hammock/settings/settings.prop</action> + <action type="set_environment"> + <environment_variable name="HHLIB" action="set_to">$INSTALL_DIR/lib/hh</environment_variable> + </action> + </actions> + </actions_group> + </install> + </package> + + + + <set_environment version="1.0"> + <environment_variable name="HAMMOCK_JAR" action="set_to">$REPOSITORY_INSTALL_DIR/Hammock/dist/Hammock.jar</environment_variable> + <environment_variable name="MATRIX_PATH" action="set_to">$REPOSITORY_INSTALL_DIR/Hammock/matrices/</environment_variable> + </set_environment> +</tool_dependency> |
| b |
| diff -r 7950e4c52972 -r 22b245c1bb94 v.1.1.0/Hammock/dist/Hammock.jar |
| b |
| Binary file v.1.1.0/Hammock/dist/Hammock.jar has changed |
| b |
| diff -r 7950e4c52972 -r 22b245c1bb94 v.1.1.0/Hammock/matrices/blosum100.txt --- a/v.1.1.0/Hammock/matrices/blosum100.txt Fri Jun 23 05:40:22 2017 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,31 +0,0 @@ -# Matrix made by matblas from blosum100_3.iij -# * column uses minimum score -# BLOSUM Clustered Scoring Matrix in 1/3 Bit Units -# Blocks Database = /data/blocks_5.0/blocks.dat -# Cluster Percentage: >= 100 -# Entropy = 1.4516, Expected = -1.0948 - A R N D C Q E G H I L K M F P S T W Y V B Z X * -A 8 -3 -4 -5 -2 -2 -3 -1 -4 -4 -4 -2 -3 -5 -2 1 -1 -6 -5 -2 -4 -2 -2 -10 -R -3 10 -2 -5 -8 0 -2 -6 -1 -7 -6 3 -4 -6 -5 -3 -3 -7 -5 -6 -4 -1 -3 -10 -N -4 -2 11 1 -5 -1 -2 -2 0 -7 -7 -1 -5 -7 -5 0 -1 -8 -5 -7 5 -2 -3 -10 -D -5 -5 1 10 -8 -2 2 -4 -3 -8 -8 -3 -8 -8 -5 -2 -4 -10 -7 -8 6 0 -4 -10 -C -2 -8 -5 -8 14 -7 -9 -7 -8 -3 -5 -8 -4 -4 -8 -3 -3 -7 -6 -3 -7 -8 -5 -10 -Q -2 0 -1 -2 -7 11 2 -5 1 -6 -5 2 -2 -6 -4 -2 -3 -5 -4 -5 -2 5 -2 -10 -E -3 -2 -2 2 -9 2 10 -6 -2 -7 -7 0 -5 -8 -4 -2 -3 -8 -7 -5 0 7 -3 -10 -G -1 -6 -2 -4 -7 -5 -6 9 -6 -9 -8 -5 -7 -8 -6 -2 -5 -7 -8 -8 -3 -5 -4 -10 -H -4 -1 0 -3 -8 1 -2 -6 13 -7 -6 -3 -5 -4 -5 -3 -4 -5 1 -7 -2 -1 -4 -10 -I -4 -7 -7 -8 -3 -6 -7 -9 -7 8 2 -6 1 -2 -7 -5 -3 -6 -4 4 -8 -7 -3 -10 -L -4 -6 -7 -8 -5 -5 -7 -8 -6 2 8 -6 3 0 -7 -6 -4 -5 -4 0 -8 -6 -3 -10 -K -2 3 -1 -3 -8 2 0 -5 -3 -6 -6 10 -4 -6 -3 -2 -3 -8 -5 -5 -2 0 -3 -10 -M -3 -4 -5 -8 -4 -2 -5 -7 -5 1 3 -4 12 -1 -5 -4 -2 -4 -5 0 -7 -4 -3 -10 -F -5 -6 -7 -8 -4 -6 -8 -8 -4 -2 0 -6 -1 11 -7 -5 -5 0 4 -3 -7 -7 -4 -10 -P -2 -5 -5 -5 -8 -4 -4 -6 -5 -7 -7 -3 -5 -7 12 -3 -4 -8 -7 -6 -5 -4 -4 -10 -S 1 -3 0 -2 -3 -2 -2 -2 -3 -5 -6 -2 -4 -5 -3 9 2 -7 -5 -4 -1 -2 -2 -10 -T -1 -3 -1 -4 -3 -3 -3 -5 -4 -3 -4 -3 -2 -5 -4 2 9 -7 -5 -1 -2 -3 -2 -10 -W -6 -7 -8 -10 -7 -5 -8 -7 -5 -6 -5 -8 -4 0 -8 -7 -7 17 2 -5 -9 -7 -6 -10 -Y -5 -5 -5 -7 -6 -4 -7 -8 1 -4 -4 -5 -5 4 -7 -5 -5 2 12 -5 -6 -6 -4 -10 -V -2 -6 -7 -8 -3 -5 -5 -8 -7 4 0 -5 0 -3 -6 -4 -1 -5 -5 8 -7 -5 -3 -10 -B -4 -4 5 6 -7 -2 0 -3 -2 -8 -8 -2 -7 -7 -5 -1 -2 -9 -6 -7 6 0 -4 -10 -Z -2 -1 -2 0 -8 5 7 -5 -1 -7 -6 0 -4 -7 -4 -2 -3 -7 -6 -5 0 6 -2 -10 -X -2 -3 -3 -4 -5 -2 -3 -4 -4 -3 -3 -3 -3 -4 -4 -2 -2 -6 -4 -3 -4 -2 -3 -10 -* -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 1 |
| b |
| diff -r 7950e4c52972 -r 22b245c1bb94 v.1.1.0/Hammock/matrices/blosum30.txt --- a/v.1.1.0/Hammock/matrices/blosum30.txt Fri Jun 23 05:40:22 2017 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,31 +0,0 @@ -# Matrix made by matblas from blosum30.iij -# * column uses minimum score -# BLOSUM Clustered Scoring Matrix in 1/5 Bit Units -# Blocks Database = /data/blocks_5.0/blocks.dat -# Cluster Percentage: >= 30 -# Entropy = 0.1424, Expected = -0.1074 - A R N D C Q E G H I L K M F P S T W Y V B Z X * -A 4 -1 0 0 -3 1 0 0 -2 0 -1 0 1 -2 -1 1 1 -5 -4 1 0 0 0 -7 -R -1 8 -2 -1 -2 3 -1 -2 -1 -3 -2 1 0 -1 -1 -1 -3 0 0 -1 -2 0 -1 -7 -N 0 -2 8 1 -1 -1 -1 0 -1 0 -2 0 0 -1 -3 0 1 -7 -4 -2 4 -1 0 -7 -D 0 -1 1 9 -3 -1 1 -1 -2 -4 -1 0 -3 -5 -1 0 -1 -4 -1 -2 5 0 -1 -7 -C -3 -2 -1 -3 17 -2 1 -4 -5 -2 0 -3 -2 -3 -3 -2 -2 -2 -6 -2 -2 0 -2 -7 -Q 1 3 -1 -1 -2 8 2 -2 0 -2 -2 0 -1 -3 0 -1 0 -1 -1 -3 -1 4 0 -7 -E 0 -1 -1 1 1 2 6 -2 0 -3 -1 2 -1 -4 1 0 -2 -1 -2 -3 0 5 -1 -7 -G 0 -2 0 -1 -4 -2 -2 8 -3 -1 -2 -1 -2 -3 -1 0 -2 1 -3 -3 0 -2 -1 -7 -H -2 -1 -1 -2 -5 0 0 -3 14 -2 -1 -2 2 -3 1 -1 -2 -5 0 -3 -2 0 -1 -7 -I 0 -3 0 -4 -2 -2 -3 -1 -2 6 2 -2 1 0 -3 -1 0 -3 -1 4 -2 -3 0 -7 -L -1 -2 -2 -1 0 -2 -1 -2 -1 2 4 -2 2 2 -3 -2 0 -2 3 1 -1 -1 0 -7 -K 0 1 0 0 -3 0 2 -1 -2 -2 -2 4 2 -1 1 0 -1 -2 -1 -2 0 1 0 -7 -M 1 0 0 -3 -2 -1 -1 -2 2 1 2 2 6 -2 -4 -2 0 -3 -1 0 -2 -1 0 -7 -F -2 -1 -1 -5 -3 -3 -4 -3 -3 0 2 -1 -2 10 -4 -1 -2 1 3 1 -3 -4 -1 -7 -P -1 -1 -3 -1 -3 0 1 -1 1 -3 -3 1 -4 -4 11 -1 0 -3 -2 -4 -2 0 -1 -7 -S 1 -1 0 0 -2 -1 0 0 -1 -1 -2 0 -2 -1 -1 4 2 -3 -2 -1 0 -1 0 -7 -T 1 -3 1 -1 -2 0 -2 -2 -2 0 0 -1 0 -2 0 2 5 -5 -1 1 0 -1 0 -7 -W -5 0 -7 -4 -2 -1 -1 1 -5 -3 -2 -2 -3 1 -3 -3 -5 20 5 -3 -5 -1 -2 -7 -Y -4 0 -4 -1 -6 -1 -2 -3 0 -1 3 -1 -1 3 -2 -2 -1 5 9 1 -3 -2 -1 -7 -V 1 -1 -2 -2 -2 -3 -3 -3 -3 4 1 -2 0 1 -4 -1 1 -3 1 5 -2 -3 0 -7 -B 0 -2 4 5 -2 -1 0 0 -2 -2 -1 0 -2 -3 -2 0 0 -5 -3 -2 5 0 -1 -7 -Z 0 0 -1 0 0 4 5 -2 0 -3 -1 1 -1 -4 0 -1 -1 -1 -2 -3 0 4 0 -7 -X 0 -1 0 -1 -2 0 -1 -1 -1 0 0 0 0 -1 -1 0 0 -2 -1 0 -1 0 -1 -7 -* -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 1 |
| b |
| diff -r 7950e4c52972 -r 22b245c1bb94 v.1.1.0/Hammock/matrices/blosum35.txt --- a/v.1.1.0/Hammock/matrices/blosum35.txt Fri Jun 23 05:40:22 2017 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,31 +0,0 @@ -# Matrix made by matblas from blosum35.iij -# * column uses minimum score -# BLOSUM Clustered Scoring Matrix in 1/4 Bit Units -# Blocks Database = /data/blocks_5.0/blocks.dat -# Cluster Percentage: >= 35 -# Entropy = 0.2111, Expected = -0.1550 - A R N D C Q E G H I L K M F P S T W Y V B Z X * -A 5 -1 -1 -1 -2 0 -1 0 -2 -1 -2 0 0 -2 -2 1 0 -2 -1 0 -1 -1 0 -5 -R -1 8 -1 -1 -3 2 -1 -2 -1 -3 -2 2 0 -1 -2 -1 -2 0 0 -1 -1 0 -1 -5 -N -1 -1 7 1 -1 1 -1 1 1 -1 -2 0 -1 -1 -2 0 0 -2 -2 -2 4 0 0 -5 -D -1 -1 1 8 -3 -1 2 -2 0 -3 -2 -1 -3 -3 -1 -1 -1 -3 -2 -2 5 1 -1 -5 -C -2 -3 -1 -3 15 -3 -1 -3 -4 -4 -2 -2 -4 -4 -4 -3 -1 -5 -5 -2 -2 -2 -2 -5 -Q 0 2 1 -1 -3 7 2 -2 -1 -2 -2 0 -1 -4 0 0 0 -1 0 -3 0 4 -1 -5 -E -1 -1 -1 2 -1 2 6 -2 -1 -3 -1 1 -2 -3 0 0 -1 -1 -1 -2 0 5 -1 -5 -G 0 -2 1 -2 -3 -2 -2 7 -2 -3 -3 -1 -1 -3 -2 1 -2 -1 -2 -3 0 -2 -1 -5 -H -2 -1 1 0 -4 -1 -1 -2 12 -3 -2 -2 1 -3 -1 -1 -2 -4 0 -4 0 -1 -1 -5 -I -1 -3 -1 -3 -4 -2 -3 -3 -3 5 2 -2 1 1 -1 -2 -1 -1 0 4 -2 -3 0 -5 -L -2 -2 -2 -2 -2 -2 -1 -3 -2 2 5 -2 3 2 -3 -2 0 0 0 2 -2 -2 0 -5 -K 0 2 0 -1 -2 0 1 -1 -2 -2 -2 5 0 -1 0 0 0 0 -1 -2 0 1 0 -5 -M 0 0 -1 -3 -4 -1 -2 -1 1 1 3 0 6 0 -3 -1 0 1 0 1 -2 -2 0 -5 -F -2 -1 -1 -3 -4 -4 -3 -3 -3 1 2 -1 0 8 -4 -1 -1 1 3 1 -2 -3 -1 -5 -P -2 -2 -2 -1 -4 0 0 -2 -1 -1 -3 0 -3 -4 10 -2 0 -4 -3 -3 -1 0 -1 -5 -S 1 -1 0 -1 -3 0 0 1 -1 -2 -2 0 -1 -1 -2 4 2 -2 -1 -1 0 0 0 -5 -T 0 -2 0 -1 -1 0 -1 -2 -2 -1 0 0 0 -1 0 2 5 -2 -2 1 -1 -1 0 -5 -W -2 0 -2 -3 -5 -1 -1 -1 -4 -1 0 0 1 1 -4 -2 -2 16 3 -2 -3 -1 -1 -5 -Y -1 0 -2 -2 -5 0 -1 -2 0 0 0 -1 0 3 -3 -1 -2 3 8 0 -2 -1 -1 -5 -V 0 -1 -2 -2 -2 -3 -2 -3 -4 4 2 -2 1 1 -3 -1 1 -2 0 5 -2 -2 0 -5 -B -1 -1 4 5 -2 0 0 0 0 -2 -2 0 -2 -2 -1 0 -1 -3 -2 -2 5 0 -1 -5 -Z -1 0 0 1 -2 4 5 -2 -1 -3 -2 1 -2 -3 0 0 -1 -1 -1 -2 0 4 0 -5 -X 0 -1 0 -1 -2 -1 -1 -1 -1 0 0 0 0 -1 -1 0 0 -1 -1 0 -1 0 -1 -5 -* -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 1 |
| b |
| diff -r 7950e4c52972 -r 22b245c1bb94 v.1.1.0/Hammock/matrices/blosum40.txt --- a/v.1.1.0/Hammock/matrices/blosum40.txt Fri Jun 23 05:40:22 2017 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,31 +0,0 @@ -# Matrix made by matblas from blosum40.iij -# * column uses minimum score -# BLOSUM Clustered Scoring Matrix in 1/4 Bit Units -# Blocks Database = /data/blocks_5.0/blocks.dat -# Cluster Percentage: >= 40 -# Entropy = 0.2851, Expected = -0.2090 - A R N D C Q E G H I L K M F P S T W Y V B Z X * -A 5 -2 -1 -1 -2 0 -1 1 -2 -1 -2 -1 -1 -3 -2 1 0 -3 -2 0 -1 -1 0 -6 -R -2 9 0 -1 -3 2 -1 -3 0 -3 -2 3 -1 -2 -3 -1 -2 -2 -1 -2 -1 0 -1 -6 -N -1 0 8 2 -2 1 -1 0 1 -2 -3 0 -2 -3 -2 1 0 -4 -2 -3 4 0 -1 -6 -D -1 -1 2 9 -2 -1 2 -2 0 -4 -3 0 -3 -4 -2 0 -1 -5 -3 -3 6 1 -1 -6 -C -2 -3 -2 -2 16 -4 -2 -3 -4 -4 -2 -3 -3 -2 -5 -1 -1 -6 -4 -2 -2 -3 -2 -6 -Q 0 2 1 -1 -4 8 2 -2 0 -3 -2 1 -1 -4 -2 1 -1 -1 -1 -3 0 4 -1 -6 -E -1 -1 -1 2 -2 2 7 -3 0 -4 -2 1 -2 -3 0 0 -1 -2 -2 -3 1 5 -1 -6 -G 1 -3 0 -2 -3 -2 -3 8 -2 -4 -4 -2 -2 -3 -1 0 -2 -2 -3 -4 -1 -2 -1 -6 -H -2 0 1 0 -4 0 0 -2 13 -3 -2 -1 1 -2 -2 -1 -2 -5 2 -4 0 0 -1 -6 -I -1 -3 -2 -4 -4 -3 -4 -4 -3 6 2 -3 1 1 -2 -2 -1 -3 0 4 -3 -4 -1 -6 -L -2 -2 -3 -3 -2 -2 -2 -4 -2 2 6 -2 3 2 -4 -3 -1 -1 0 2 -3 -2 -1 -6 -K -1 3 0 0 -3 1 1 -2 -1 -3 -2 6 -1 -3 -1 0 0 -2 -1 -2 0 1 -1 -6 -M -1 -1 -2 -3 -3 -1 -2 -2 1 1 3 -1 7 0 -2 -2 -1 -2 1 1 -3 -2 0 -6 -F -3 -2 -3 -4 -2 -4 -3 -3 -2 1 2 -3 0 9 -4 -2 -1 1 4 0 -3 -4 -1 -6 -P -2 -3 -2 -2 -5 -2 0 -1 -2 -2 -4 -1 -2 -4 11 -1 0 -4 -3 -3 -2 -1 -2 -6 -S 1 -1 1 0 -1 1 0 0 -1 -2 -3 0 -2 -2 -1 5 2 -5 -2 -1 0 0 0 -6 -T 0 -2 0 -1 -1 -1 -1 -2 -2 -1 -1 0 -1 -1 0 2 6 -4 -1 1 0 -1 0 -6 -W -3 -2 -4 -5 -6 -1 -2 -2 -5 -3 -1 -2 -2 1 -4 -5 -4 19 3 -3 -4 -2 -2 -6 -Y -2 -1 -2 -3 -4 -1 -2 -3 2 0 0 -1 1 4 -3 -2 -1 3 9 -1 -3 -2 -1 -6 -V 0 -2 -3 -3 -2 -3 -3 -4 -4 4 2 -2 1 0 -3 -1 1 -3 -1 5 -3 -3 -1 -6 -B -1 -1 4 6 -2 0 1 -1 0 -3 -3 0 -3 -3 -2 0 0 -4 -3 -3 5 2 -1 -6 -Z -1 0 0 1 -3 4 5 -2 0 -4 -2 1 -2 -4 -1 0 -1 -2 -2 -3 2 5 -1 -6 -X 0 -1 -1 -1 -2 -1 -1 -1 -1 -1 -1 -1 0 -1 -2 0 0 -2 -1 -1 -1 -1 -1 -6 -* -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 1 |
| b |
| diff -r 7950e4c52972 -r 22b245c1bb94 v.1.1.0/Hammock/matrices/blosum45.txt --- a/v.1.1.0/Hammock/matrices/blosum45.txt Fri Jun 23 05:40:22 2017 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,31 +0,0 @@ -# Matrix made by matblas from blosum45.iij -# * column uses minimum score -# BLOSUM Clustered Scoring Matrix in 1/3 Bit Units -# Blocks Database = /data/blocks_5.0/blocks.dat -# Cluster Percentage: >= 45 -# Entropy = 0.3795, Expected = -0.2789 - A R N D C Q E G H I L K M F P S T W Y V B Z X * -A 5 -2 -1 -2 -1 -1 -1 0 -2 -1 -1 -1 -1 -2 -1 1 0 -2 -2 0 -1 -1 0 -5 -R -2 7 0 -1 -3 1 0 -2 0 -3 -2 3 -1 -2 -2 -1 -1 -2 -1 -2 -1 0 -1 -5 -N -1 0 6 2 -2 0 0 0 1 -2 -3 0 -2 -2 -2 1 0 -4 -2 -3 4 0 -1 -5 -D -2 -1 2 7 -3 0 2 -1 0 -4 -3 0 -3 -4 -1 0 -1 -4 -2 -3 5 1 -1 -5 -C -1 -3 -2 -3 12 -3 -3 -3 -3 -3 -2 -3 -2 -2 -4 -1 -1 -5 -3 -1 -2 -3 -2 -5 -Q -1 1 0 0 -3 6 2 -2 1 -2 -2 1 0 -4 -1 0 -1 -2 -1 -3 0 4 -1 -5 -E -1 0 0 2 -3 2 6 -2 0 -3 -2 1 -2 -3 0 0 -1 -3 -2 -3 1 4 -1 -5 -G 0 -2 0 -1 -3 -2 -2 7 -2 -4 -3 -2 -2 -3 -2 0 -2 -2 -3 -3 -1 -2 -1 -5 -H -2 0 1 0 -3 1 0 -2 10 -3 -2 -1 0 -2 -2 -1 -2 -3 2 -3 0 0 -1 -5 -I -1 -3 -2 -4 -3 -2 -3 -4 -3 5 2 -3 2 0 -2 -2 -1 -2 0 3 -3 -3 -1 -5 -L -1 -2 -3 -3 -2 -2 -2 -3 -2 2 5 -3 2 1 -3 -3 -1 -2 0 1 -3 -2 -1 -5 -K -1 3 0 0 -3 1 1 -2 -1 -3 -3 5 -1 -3 -1 -1 -1 -2 -1 -2 0 1 -1 -5 -M -1 -1 -2 -3 -2 0 -2 -2 0 2 2 -1 6 0 -2 -2 -1 -2 0 1 -2 -1 -1 -5 -F -2 -2 -2 -4 -2 -4 -3 -3 -2 0 1 -3 0 8 -3 -2 -1 1 3 0 -3 -3 -1 -5 -P -1 -2 -2 -1 -4 -1 0 -2 -2 -2 -3 -1 -2 -3 9 -1 -1 -3 -3 -3 -2 -1 -1 -5 -S 1 -1 1 0 -1 0 0 0 -1 -2 -3 -1 -2 -2 -1 4 2 -4 -2 -1 0 0 0 -5 -T 0 -1 0 -1 -1 -1 -1 -2 -2 -1 -1 -1 -1 -1 -1 2 5 -3 -1 0 0 -1 0 -5 -W -2 -2 -4 -4 -5 -2 -3 -2 -3 -2 -2 -2 -2 1 -3 -4 -3 15 3 -3 -4 -2 -2 -5 -Y -2 -1 -2 -2 -3 -1 -2 -3 2 0 0 -1 0 3 -3 -2 -1 3 8 -1 -2 -2 -1 -5 -V 0 -2 -3 -3 -1 -3 -3 -3 -3 3 1 -2 1 0 -3 -1 0 -3 -1 5 -3 -3 -1 -5 -B -1 -1 4 5 -2 0 1 -1 0 -3 -3 0 -2 -3 -2 0 0 -4 -2 -3 4 2 -1 -5 -Z -1 0 0 1 -3 4 4 -2 0 -3 -2 1 -1 -3 -1 0 -1 -2 -2 -3 2 4 -1 -5 -X 0 -1 -1 -1 -2 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 0 0 -2 -1 -1 -1 -1 -1 -5 -* -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 1 |
| b |
| diff -r 7950e4c52972 -r 22b245c1bb94 v.1.1.0/Hammock/matrices/blosum50.txt --- a/v.1.1.0/Hammock/matrices/blosum50.txt Fri Jun 23 05:40:22 2017 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,31 +0,0 @@ -# Matrix made by matblas from blosum50.iij -# * column uses minimum score -# BLOSUM Clustered Scoring Matrix in 1/3 Bit Units -# Blocks Database = /data/blocks_5.0/blocks.dat -# Cluster Percentage: >= 50 -# Entropy = 0.4808, Expected = -0.3573 - A R N D C Q E G H I L K M F P S T W Y V B Z X * -A 5 -2 -1 -2 -1 -1 -1 0 -2 -1 -2 -1 -1 -3 -1 1 0 -3 -2 0 -2 -1 -1 -5 -R -2 7 -1 -2 -4 1 0 -3 0 -4 -3 3 -2 -3 -3 -1 -1 -3 -1 -3 -1 0 -1 -5 -N -1 -1 7 2 -2 0 0 0 1 -3 -4 0 -2 -4 -2 1 0 -4 -2 -3 4 0 -1 -5 -D -2 -2 2 8 -4 0 2 -1 -1 -4 -4 -1 -4 -5 -1 0 -1 -5 -3 -4 5 1 -1 -5 -C -1 -4 -2 -4 13 -3 -3 -3 -3 -2 -2 -3 -2 -2 -4 -1 -1 -5 -3 -1 -3 -3 -2 -5 -Q -1 1 0 0 -3 7 2 -2 1 -3 -2 2 0 -4 -1 0 -1 -1 -1 -3 0 4 -1 -5 -E -1 0 0 2 -3 2 6 -3 0 -4 -3 1 -2 -3 -1 -1 -1 -3 -2 -3 1 5 -1 -5 -G 0 -3 0 -1 -3 -2 -3 8 -2 -4 -4 -2 -3 -4 -2 0 -2 -3 -3 -4 -1 -2 -2 -5 -H -2 0 1 -1 -3 1 0 -2 10 -4 -3 0 -1 -1 -2 -1 -2 -3 2 -4 0 0 -1 -5 -I -1 -4 -3 -4 -2 -3 -4 -4 -4 5 2 -3 2 0 -3 -3 -1 -3 -1 4 -4 -3 -1 -5 -L -2 -3 -4 -4 -2 -2 -3 -4 -3 2 5 -3 3 1 -4 -3 -1 -2 -1 1 -4 -3 -1 -5 -K -1 3 0 -1 -3 2 1 -2 0 -3 -3 6 -2 -4 -1 0 -1 -3 -2 -3 0 1 -1 -5 -M -1 -2 -2 -4 -2 0 -2 -3 -1 2 3 -2 7 0 -3 -2 -1 -1 0 1 -3 -1 -1 -5 -F -3 -3 -4 -5 -2 -4 -3 -4 -1 0 1 -4 0 8 -4 -3 -2 1 4 -1 -4 -4 -2 -5 -P -1 -3 -2 -1 -4 -1 -1 -2 -2 -3 -4 -1 -3 -4 10 -1 -1 -4 -3 -3 -2 -1 -2 -5 -S 1 -1 1 0 -1 0 -1 0 -1 -3 -3 0 -2 -3 -1 5 2 -4 -2 -2 0 0 -1 -5 -T 0 -1 0 -1 -1 -1 -1 -2 -2 -1 -1 -1 -1 -2 -1 2 5 -3 -2 0 0 -1 0 -5 -W -3 -3 -4 -5 -5 -1 -3 -3 -3 -3 -2 -3 -1 1 -4 -4 -3 15 2 -3 -5 -2 -3 -5 -Y -2 -1 -2 -3 -3 -1 -2 -3 2 -1 -1 -2 0 4 -3 -2 -2 2 8 -1 -3 -2 -1 -5 -V 0 -3 -3 -4 -1 -3 -3 -4 -4 4 1 -3 1 -1 -3 -2 0 -3 -1 5 -4 -3 -1 -5 -B -2 -1 4 5 -3 0 1 -1 0 -4 -4 0 -3 -4 -2 0 0 -5 -3 -4 5 2 -1 -5 -Z -1 0 0 1 -3 4 5 -2 0 -3 -3 1 -1 -4 -1 0 -1 -2 -2 -3 2 5 -1 -5 -X -1 -1 -1 -1 -2 -1 -1 -2 -1 -1 -1 -1 -1 -2 -2 -1 0 -3 -1 -1 -1 -1 -1 -5 -* -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 1 |
| b |
| diff -r 7950e4c52972 -r 22b245c1bb94 v.1.1.0/Hammock/matrices/blosum55.txt --- a/v.1.1.0/Hammock/matrices/blosum55.txt Fri Jun 23 05:40:22 2017 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,31 +0,0 @@ -# Matrix made by matblas from blosum55.iij -# * column uses minimum score -# BLOSUM Clustered Scoring Matrix in 1/3 Bit Units -# Blocks Database = /data/blocks_5.0/blocks.dat -# Cluster Percentage: >= 55 -# Entropy = 0.5637, Expected = -0.4179 - A R N D C Q E G H I L K M F P S T W Y V B Z X * -A 5 -2 -2 -2 0 -1 -1 0 -2 -2 -2 -1 -1 -3 -1 2 0 -4 -2 0 -2 -1 -1 -5 -R -2 8 -1 -2 -4 1 0 -3 0 -4 -3 3 -2 -3 -3 -1 -1 -3 -2 -3 -1 0 -1 -5 -N -2 -1 8 2 -3 0 0 0 1 -4 -4 0 -3 -4 -2 1 0 -5 -2 -4 4 0 -1 -5 -D -2 -2 2 8 -4 0 2 -2 -1 -4 -5 -1 -4 -5 -2 0 -1 -5 -3 -4 5 1 -2 -5 -C 0 -4 -3 -4 13 -4 -4 -3 -4 -2 -2 -4 -2 -3 -3 -1 -1 -4 -3 -1 -4 -4 -2 -5 -Q -1 1 0 0 -4 7 2 -2 1 -4 -3 2 0 -4 -1 0 -1 -2 -1 -3 0 4 -1 -5 -E -1 0 0 2 -4 2 7 -3 -1 -4 -4 1 -3 -4 -1 0 -1 -3 -2 -3 1 5 -1 -5 -G 0 -3 0 -2 -3 -2 -3 8 -2 -5 -5 -2 -3 -4 -3 0 -2 -3 -4 -4 -1 -3 -2 -5 -H -2 0 1 -1 -4 1 -1 -2 11 -4 -3 0 -2 -1 -3 -1 -2 -3 2 -4 0 0 -1 -5 -I -2 -4 -4 -4 -2 -4 -4 -5 -4 6 2 -4 2 0 -3 -3 -1 -3 -1 4 -4 -4 -1 -5 -L -2 -3 -4 -5 -2 -3 -4 -5 -3 2 6 -3 3 1 -4 -3 -2 -3 -1 1 -4 -3 -1 -5 -K -1 3 0 -1 -4 2 1 -2 0 -4 -3 6 -2 -4 -1 0 -1 -4 -2 -3 0 1 -1 -5 -M -1 -2 -3 -4 -2 0 -3 -3 -2 2 3 -2 8 0 -3 -2 -1 -2 -1 1 -3 -2 -1 -5 -F -3 -3 -4 -5 -3 -4 -4 -4 -1 0 1 -4 0 9 -5 -3 -3 2 4 -1 -5 -4 -2 -5 -P -1 -3 -2 -2 -3 -1 -1 -3 -3 -3 -4 -1 -3 -5 10 -1 -1 -5 -4 -3 -2 -1 -2 -5 -S 2 -1 1 0 -1 0 0 0 -1 -3 -3 0 -2 -3 -1 5 2 -4 -2 -2 0 0 -1 -5 -T 0 -1 0 -1 -1 -1 -1 -2 -2 -1 -2 -1 -1 -3 -1 2 6 -3 -2 0 -1 -1 -1 -5 -W -4 -3 -5 -5 -4 -2 -3 -3 -3 -3 -3 -4 -2 2 -5 -4 -3 15 3 -4 -5 -3 -3 -5 -Y -2 -2 -2 -3 -3 -1 -2 -4 2 -1 -1 -2 -1 4 -4 -2 -2 3 9 -2 -3 -2 -1 -5 -V 0 -3 -4 -4 -1 -3 -3 -4 -4 4 1 -3 1 -1 -3 -2 0 -4 -2 5 -4 -3 -1 -5 -B -2 -1 4 5 -4 0 1 -1 0 -4 -4 0 -3 -5 -2 0 -1 -5 -3 -4 5 2 -1 -5 -Z -1 0 0 1 -4 4 5 -3 0 -4 -3 1 -2 -4 -1 0 -1 -3 -2 -3 2 5 -1 -5 -X -1 -1 -1 -2 -2 -1 -1 -2 -1 -1 -1 -1 -1 -2 -2 -1 -1 -3 -1 -1 -1 -1 -1 -5 -* -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 1 |
| b |
| diff -r 7950e4c52972 -r 22b245c1bb94 v.1.1.0/Hammock/matrices/blosum60.txt --- a/v.1.1.0/Hammock/matrices/blosum60.txt Fri Jun 23 05:40:22 2017 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,31 +0,0 @@ -# Matrix made by matblas from blosum60.iij -# * column uses minimum score -# BLOSUM Clustered Scoring Matrix in 1/2 Bit Units -# Blocks Database = /data/blocks_5.0/blocks.dat -# Cluster Percentage: >= 60 -# Entropy = 0.6603, Expected = -0.4917 - A R N D C Q E G H I L K M F P S T W Y V B Z X * -A 4 -1 -1 -2 0 -1 -1 0 -2 -1 -1 -1 -1 -2 -1 1 0 -3 -2 0 -2 -1 0 -4 -R -1 5 0 -1 -3 1 0 -2 0 -3 -2 2 -1 -3 -2 -1 -1 -3 -2 -2 -1 0 -1 -4 -N -1 0 6 1 -2 0 0 0 1 -3 -3 0 -2 -3 -2 1 0 -4 -2 -3 3 0 -1 -4 -D -2 -1 1 6 -3 0 2 -1 -1 -3 -3 -1 -3 -3 -1 0 -1 -4 -3 -3 4 1 -1 -4 -C 0 -3 -2 -3 9 -3 -3 -2 -3 -1 -1 -3 -1 -2 -3 -1 -1 -2 -2 -1 -3 -3 -2 -4 -Q -1 1 0 0 -3 5 2 -2 1 -3 -2 1 0 -3 -1 0 -1 -2 -1 -2 0 3 -1 -4 -E -1 0 0 2 -3 2 5 -2 0 -3 -3 1 -2 -3 -1 0 -1 -3 -2 -2 1 4 -1 -4 -G 0 -2 0 -1 -2 -2 -2 6 -2 -3 -4 -1 -2 -3 -2 0 -2 -2 -3 -3 -1 -2 -1 -4 -H -2 0 1 -1 -3 1 0 -2 7 -3 -3 -1 -1 -1 -2 -1 -2 -2 2 -3 0 0 -1 -4 -I -1 -3 -3 -3 -1 -3 -3 -3 -3 4 2 -3 1 0 -3 -2 -1 -2 -1 3 -3 -3 -1 -4 -L -1 -2 -3 -3 -1 -2 -3 -4 -3 2 4 -2 2 0 -3 -2 -1 -2 -1 1 -3 -2 -1 -4 -K -1 2 0 -1 -3 1 1 -1 -1 -3 -2 4 -1 -3 -1 0 -1 -3 -2 -2 0 1 -1 -4 -M -1 -1 -2 -3 -1 0 -2 -2 -1 1 2 -1 5 0 -2 -1 -1 -1 -1 1 -3 -1 -1 -4 -F -2 -3 -3 -3 -2 -3 -3 -3 -1 0 0 -3 0 6 -4 -2 -2 1 3 -1 -3 -3 -1 -4 -P -1 -2 -2 -1 -3 -1 -1 -2 -2 -3 -3 -1 -2 -4 7 -1 -1 -4 -3 -2 -2 -1 -2 -4 -S 1 -1 1 0 -1 0 0 0 -1 -2 -2 0 -1 -2 -1 4 1 -3 -2 -2 0 0 0 -4 -T 0 -1 0 -1 -1 -1 -1 -2 -2 -1 -1 -1 -1 -2 -1 1 4 -2 -2 0 0 -1 0 -4 -W -3 -3 -4 -4 -2 -2 -3 -2 -2 -2 -2 -3 -1 1 -4 -3 -2 10 2 -3 -4 -2 -2 -4 -Y -2 -2 -2 -3 -2 -1 -2 -3 2 -1 -1 -2 -1 3 -3 -2 -2 2 6 -1 -2 -2 -1 -4 -V 0 -2 -3 -3 -1 -2 -2 -3 -3 3 1 -2 1 -1 -2 -2 0 -3 -1 4 -3 -2 -1 -4 -B -2 -1 3 4 -3 0 1 -1 0 -3 -3 0 -3 -3 -2 0 0 -4 -2 -3 4 1 -1 -4 -Z -1 0 0 1 -3 3 4 -2 0 -3 -2 1 -1 -3 -1 0 -1 -2 -2 -2 1 3 -1 -4 -X 0 -1 -1 -1 -2 -1 -1 -1 -1 -1 -1 -1 -1 -1 -2 0 0 -2 -1 -1 -1 -1 -1 -4 -* -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 1 |
| b |
| diff -r 7950e4c52972 -r 22b245c1bb94 v.1.1.0/Hammock/matrices/blosum62.txt --- a/v.1.1.0/Hammock/matrices/blosum62.txt Fri Jun 23 05:40:22 2017 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,31 +0,0 @@ -# Matrix made by matblas from blosum62.iij -# * column uses minimum score -# BLOSUM Clustered Scoring Matrix in 1/2 Bit Units -# Blocks Database = /data/blocks_5.0/blocks.dat -# Cluster Percentage: >= 62 -# Entropy = 0.6979, Expected = -0.5209 - A R N D C Q E G H I L K M F P S T W Y V B Z X * -A 4 -1 -2 -2 0 -1 -1 0 -2 -1 -1 -1 -1 -2 -1 1 0 -3 -2 0 -2 -1 0 -4 -R -1 5 0 -2 -3 1 0 -2 0 -3 -2 2 -1 -3 -2 -1 -1 -3 -2 -3 -1 0 -1 -4 -N -2 0 6 1 -3 0 0 0 1 -3 -3 0 -2 -3 -2 1 0 -4 -2 -3 3 0 -1 -4 -D -2 -2 1 6 -3 0 2 -1 -1 -3 -4 -1 -3 -3 -1 0 -1 -4 -3 -3 4 1 -1 -4 -C 0 -3 -3 -3 9 -3 -4 -3 -3 -1 -1 -3 -1 -2 -3 -1 -1 -2 -2 -1 -3 -3 -2 -4 -Q -1 1 0 0 -3 5 2 -2 0 -3 -2 1 0 -3 -1 0 -1 -2 -1 -2 0 3 -1 -4 -E -1 0 0 2 -4 2 5 -2 0 -3 -3 1 -2 -3 -1 0 -1 -3 -2 -2 1 4 -1 -4 -G 0 -2 0 -1 -3 -2 -2 6 -2 -4 -4 -2 -3 -3 -2 0 -2 -2 -3 -3 -1 -2 -1 -4 -H -2 0 1 -1 -3 0 0 -2 8 -3 -3 -1 -2 -1 -2 -1 -2 -2 2 -3 0 0 -1 -4 -I -1 -3 -3 -3 -1 -3 -3 -4 -3 4 2 -3 1 0 -3 -2 -1 -3 -1 3 -3 -3 -1 -4 -L -1 -2 -3 -4 -1 -2 -3 -4 -3 2 4 -2 2 0 -3 -2 -1 -2 -1 1 -4 -3 -1 -4 -K -1 2 0 -1 -3 1 1 -2 -1 -3 -2 5 -1 -3 -1 0 -1 -3 -2 -2 0 1 -1 -4 -M -1 -1 -2 -3 -1 0 -2 -3 -2 1 2 -1 5 0 -2 -1 -1 -1 -1 1 -3 -1 -1 -4 -F -2 -3 -3 -3 -2 -3 -3 -3 -1 0 0 -3 0 6 -4 -2 -2 1 3 -1 -3 -3 -1 -4 -P -1 -2 -2 -1 -3 -1 -1 -2 -2 -3 -3 -1 -2 -4 7 -1 -1 -4 -3 -2 -2 -1 -2 -4 -S 1 -1 1 0 -1 0 0 0 -1 -2 -2 0 -1 -2 -1 4 1 -3 -2 -2 0 0 0 -4 -T 0 -1 0 -1 -1 -1 -1 -2 -2 -1 -1 -1 -1 -2 -1 1 5 -2 -2 0 -1 -1 0 -4 -W -3 -3 -4 -4 -2 -2 -3 -2 -2 -3 -2 -3 -1 1 -4 -3 -2 11 2 -3 -4 -3 -2 -4 -Y -2 -2 -2 -3 -2 -1 -2 -3 2 -1 -1 -2 -1 3 -3 -2 -2 2 7 -1 -3 -2 -1 -4 -V 0 -3 -3 -3 -1 -2 -2 -3 -3 3 1 -2 1 -1 -2 -2 0 -3 -1 4 -3 -2 -1 -4 -B -2 -1 3 4 -3 0 1 -1 0 -3 -4 0 -3 -3 -2 0 -1 -4 -3 -3 4 1 -1 -4 -Z -1 0 0 1 -3 3 4 -2 0 -3 -3 1 -1 -3 -1 0 -1 -3 -2 -2 1 4 -1 -4 -X 0 -1 -1 -1 -2 -1 -1 -1 -1 -1 -1 -1 -1 -1 -2 0 0 -2 -1 -1 -1 -1 -1 -4 -* -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 1 |
| b |
| diff -r 7950e4c52972 -r 22b245c1bb94 v.1.1.0/Hammock/matrices/blosum62.txt~ --- a/v.1.1.0/Hammock/matrices/blosum62.txt~ Fri Jun 23 05:40:22 2017 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,31 +0,0 @@ -# Matrix made by matblas from blosum62.iij -# * column uses minimum score -# BLOSUM Clustered Scoring Matrix in 1/2 Bit Units -# Blocks Database = /data/blocks_5.0/blocks.dat -# Cluster Percentage: >= 62 -# Entropy = 0.6979, Expected = -0.5209 - A R N D C Q E G H I L K M F P S T W Y V B Z X * -A 4 -1 -2 -2 0 -1 -1 0 -2 -1 -1 -1 -1 -2 -1 1 0 -3 -2 0 -2 -1 0 -4 -R -1 5 0 -2 -3 1 0 -2 0 -3 -2 2 -1 -3 -2 -1 -1 -3 -2 -3 -1 0 -1 -4 -N -2 0 6 1 -3 0 0 0 1 -3 -3 0 -2 -3 -2 1 0 -4 -2 -3 3 0 -1 -4 -D -2 -2 1 6 -3 0 2 -1 -1 -3 -4 -1 -3 -3 -1 0 -1 -4 -3 -3 4 1 -1 -4 -C 0 -3 -3 -3 9 -3 -4 -3 -3 -1 -1 -3 -1 -2 -3 -1 -1 -2 -2 -1 -3 -3 -2 -4 -Q -1 1 0 0 -3 5 2 -2 0 -3 -2 1 0 -3 -1 0 -1 -2 -1 -2 0 3 -1 -4 -E -1 0 0 2 -4 2 5 -2 0 -3 -3 1 -2 -3 -1 0 -1 -3 -2 -2 1 4 -1 -4 -G 0 -2 0 -1 -3 -2 -2 6 -2 -4 -4 -2 -3 -3 -2 0 -2 -2 -3 -3 -1 -2 -1 -4 -H -2 0 1 -1 -3 0 0 -2 8 -3 -3 -1 -2 -1 -2 -1 -2 -2 2 -3 0 0 -1 -4 -I -1 -3 -3 -3 -1 -3 -3 -4 -3 4 2 -3 1 0 -3 -2 -1 -3 -1 3 -3 -3 -1 -4 -L -1 -2 -3 -4 -1 -2 -3 -4 -3 2 4 -2 2 0 -3 -2 -1 -2 -1 1 -4 -3 -1 -4 -K -1 2 0 -1 -3 1 1 -2 -1 -3 -2 5 -1 -3 -1 0 -1 -3 -2 -2 0 1 -1 -4 -M -1 -1 -2 -3 -1 0 -2 -3 -2 1 2 -1 5 0 -2 -1 -1 -1 -1 1 -3 -1 -1 -4 -F -2 -3 -3 -3 -2 -3 -3 -3 -1 0 0 -3 0 6 -4 -2 -2 1 3 -1 -3 -3 -1 -4 -P -1 -2 -2 -1 -3 -1 -1 -2 -2 -3 -3 -1 -2 -4 7 -1 -1 -4 -3 -2 -2 -1 -2 -4 -S 1 -1 1 0 -1 0 0 0 -1 -2 -2 0 -1 -2 -1 4 1 -3 -2 -2 0 0 0 -4 -T 0 -1 0 -1 -1 -1 -1 -2 -2 -1 -1 -1 -1 -2 -1 1 5 -2 -2 0 -1 -1 0 -4 -W -3 -3 -4 -4 -2 -2 -3 -2 -2 -3 -2 -3 -1 1 -4 -3 -2 11 2 -3 -4 -3 -2 -4 -Y -2 -2 -2 -3 -2 -1 -2 -3 2 -1 -1 -2 -1 3 -3 -2 -2 2 7 -1 -3 -2 -1 -4 -V 0 -3 -3 -3 -1 -2 -2 -3 -3 3 1 -2 1 -1 -2 -2 0 -3 -1 4 -3 -2 -1 -4 -B -2 -1 3 4 -3 0 1 -1 0 -3 -4 0 -3 -3 -2 0 -1 -4 -3 -3 4 1 -1 -4 -Z -1 0 0 1 -3 3 4 -2 0 -3 -3 1 -1 -3 -1 0 -1 -3 -2 -2 1 4 -1 -4 -X 0 -1 -1 -1 -2 -1 -1 -1 -1 -1 -1 -1 -1 -1 -2 0 0 -2 -1 -1 -1 -1 -1 -4 -* -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 1 |
| b |
| diff -r 7950e4c52972 -r 22b245c1bb94 v.1.1.0/Hammock/matrices/blosum65.txt --- a/v.1.1.0/Hammock/matrices/blosum65.txt Fri Jun 23 05:40:22 2017 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,31 +0,0 @@ -# Matrix made by matblas from blosum65.iij -# * column uses minimum score -# BLOSUM Clustered Scoring Matrix in 1/2 Bit Units -# Blocks Database = /data/blocks_5.0/blocks.dat -# Cluster Percentage: >= 65 -# Entropy = 0.7576, Expected = -0.5675 - A R N D C Q E G H I L K M F P S T W Y V B Z X * -A 4 -1 -2 -2 0 -1 -1 0 -2 -1 -2 -1 -1 -2 -1 1 0 -3 -2 0 -2 -1 -1 -5 -R -1 6 0 -2 -4 1 0 -2 0 -3 -2 2 -2 -3 -2 -1 -1 -3 -2 -3 -1 0 -1 -5 -N -2 0 6 1 -3 0 0 -1 1 -3 -4 0 -2 -3 -2 1 0 -4 -2 -3 3 0 -1 -5 -D -2 -2 1 6 -4 0 2 -1 -1 -3 -4 -1 -3 -4 -2 0 -1 -5 -3 -3 4 1 -1 -5 -C 0 -4 -3 -4 9 -3 -4 -3 -3 -1 -1 -3 -2 -2 -3 -1 -1 -2 -2 -1 -3 -4 -2 -5 -Q -1 1 0 0 -3 6 2 -2 1 -3 -2 1 0 -3 -1 0 -1 -2 -2 -2 0 3 -1 -5 -E -1 0 0 2 -4 2 5 -2 0 -3 -3 1 -2 -3 -1 0 -1 -3 -2 -3 1 4 -1 -5 -G 0 -2 -1 -1 -3 -2 -2 6 -2 -4 -4 -2 -3 -3 -2 0 -2 -3 -3 -3 -1 -2 -2 -5 -H -2 0 1 -1 -3 1 0 -2 8 -3 -3 -1 -2 -1 -2 -1 -2 -2 2 -3 0 0 -1 -5 -I -1 -3 -3 -3 -1 -3 -3 -4 -3 4 2 -3 1 0 -3 -2 -1 -2 -1 3 -3 -3 -1 -5 -L -2 -2 -4 -4 -1 -2 -3 -4 -3 2 4 -3 2 0 -3 -3 -1 -2 -1 1 -4 -3 -1 -5 -K -1 2 0 -1 -3 1 1 -2 -1 -3 -3 5 -2 -3 -1 0 -1 -3 -2 -2 0 1 -1 -5 -M -1 -2 -2 -3 -2 0 -2 -3 -2 1 2 -2 6 0 -3 -2 -1 -2 -1 1 -3 -2 -1 -5 -F -2 -3 -3 -4 -2 -3 -3 -3 -1 0 0 -3 0 6 -4 -2 -2 1 3 -1 -3 -3 -2 -5 -P -1 -2 -2 -2 -3 -1 -1 -2 -2 -3 -3 -1 -3 -4 8 -1 -1 -4 -3 -2 -2 -1 -2 -5 -S 1 -1 1 0 -1 0 0 0 -1 -2 -3 0 -2 -2 -1 4 1 -3 -2 -2 0 0 -1 -5 -T 0 -1 0 -1 -1 -1 -1 -2 -2 -1 -1 -1 -1 -2 -1 1 5 -3 -2 0 -1 -1 -1 -5 -W -3 -3 -4 -5 -2 -2 -3 -3 -2 -2 -2 -3 -2 1 -4 -3 -3 10 2 -3 -4 -3 -2 -5 -Y -2 -2 -2 -3 -2 -2 -2 -3 2 -1 -1 -2 -1 3 -3 -2 -2 2 7 -1 -3 -2 -1 -5 -V 0 -3 -3 -3 -1 -2 -3 -3 -3 3 1 -2 1 -1 -2 -2 0 -3 -1 4 -3 -2 -1 -5 -B -2 -1 3 4 -3 0 1 -1 0 -3 -4 0 -3 -3 -2 0 -1 -4 -3 -3 4 1 -1 -5 -Z -1 0 0 1 -4 3 4 -2 0 -3 -3 1 -2 -3 -1 0 -1 -3 -2 -2 1 4 -1 -5 -X -1 -1 -1 -1 -2 -1 -1 -2 -1 -1 -1 -1 -1 -2 -2 -1 -1 -2 -1 -1 -1 -1 -1 -5 -* -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 1 |
| b |
| diff -r 7950e4c52972 -r 22b245c1bb94 v.1.1.0/Hammock/matrices/blosum70.txt --- a/v.1.1.0/Hammock/matrices/blosum70.txt Fri Jun 23 05:40:22 2017 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,31 +0,0 @@ -# Matrix made by matblas from blosum70.iij -# * column uses minimum score -# BLOSUM Clustered Scoring Matrix in 1/2 Bit Units -# Blocks Database = /data/blocks_5.0/blocks.dat -# Cluster Percentage: >= 70 -# Entropy = 0.8391, Expected = -0.6313 - A R N D C Q E G H I L K M F P S T W Y V B Z X * -A 4 -2 -2 -2 -1 -1 -1 0 -2 -2 -2 -1 -1 -2 -1 1 0 -3 -2 0 -2 -1 -1 -5 -R -2 6 -1 -2 -4 1 0 -3 0 -3 -3 2 -2 -3 -2 -1 -1 -3 -2 -3 -1 0 -1 -5 -N -2 -1 6 1 -3 0 0 -1 0 -4 -4 0 -2 -3 -2 0 0 -4 -2 -3 3 0 -1 -5 -D -2 -2 1 6 -4 -1 1 -2 -1 -4 -4 -1 -3 -4 -2 0 -1 -5 -4 -4 4 1 -2 -5 -C -1 -4 -3 -4 9 -3 -4 -3 -4 -1 -2 -4 -2 -2 -3 -1 -1 -3 -3 -1 -4 -4 -2 -5 -Q -1 1 0 -1 -3 6 2 -2 1 -3 -2 1 0 -3 -2 0 -1 -2 -2 -2 0 3 -1 -5 -E -1 0 0 1 -4 2 5 -2 0 -4 -3 1 -2 -4 -1 0 -1 -4 -3 -3 1 4 -1 -5 -G 0 -3 -1 -2 -3 -2 -2 6 -2 -4 -4 -2 -3 -4 -3 -1 -2 -3 -4 -4 -1 -2 -2 -5 -H -2 0 0 -1 -4 1 0 -2 8 -4 -3 -1 -2 -1 -2 -1 -2 -2 2 -3 -1 0 -1 -5 -I -2 -3 -4 -4 -1 -3 -4 -4 -4 4 2 -3 1 0 -3 -3 -1 -3 -1 3 -4 -3 -1 -5 -L -2 -3 -4 -4 -2 -2 -3 -4 -3 2 4 -3 2 0 -3 -3 -2 -2 -1 1 -4 -3 -1 -5 -K -1 2 0 -1 -4 1 1 -2 -1 -3 -3 5 -2 -3 -1 0 -1 -3 -2 -3 -1 1 -1 -5 -M -1 -2 -2 -3 -2 0 -2 -3 -2 1 2 -2 6 0 -3 -2 -1 -2 -1 1 -3 -2 -1 -5 -F -2 -3 -3 -4 -2 -3 -4 -4 -1 0 0 -3 0 6 -4 -3 -2 1 3 -1 -4 -4 -2 -5 -P -1 -2 -2 -2 -3 -2 -1 -3 -2 -3 -3 -1 -3 -4 8 -1 -1 -4 -3 -3 -2 -1 -2 -5 -S 1 -1 0 0 -1 0 0 -1 -1 -3 -3 0 -2 -3 -1 4 1 -3 -2 -2 0 0 -1 -5 -T 0 -1 0 -1 -1 -1 -1 -2 -2 -1 -2 -1 -1 -2 -1 1 5 -3 -2 0 -1 -1 -1 -5 -W -3 -3 -4 -5 -3 -2 -4 -3 -2 -3 -2 -3 -2 1 -4 -3 -3 11 2 -3 -4 -3 -3 -5 -Y -2 -2 -2 -4 -3 -2 -3 -4 2 -1 -1 -2 -1 3 -3 -2 -2 2 7 -2 -3 -2 -2 -5 -V 0 -3 -3 -4 -1 -2 -3 -4 -3 3 1 -3 1 -1 -3 -2 0 -3 -2 4 -3 -3 -1 -5 -B -2 -1 3 4 -4 0 1 -1 -1 -4 -4 -1 -3 -4 -2 0 -1 -4 -3 -3 4 0 -1 -5 -Z -1 0 0 1 -4 3 4 -2 0 -3 -3 1 -2 -4 -1 0 -1 -3 -2 -3 0 4 -1 -5 -X -1 -1 -1 -2 -2 -1 -1 -2 -1 -1 -1 -1 -1 -2 -2 -1 -1 -3 -2 -1 -1 -1 -1 -5 -* -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 1 |
| b |
| diff -r 7950e4c52972 -r 22b245c1bb94 v.1.1.0/Hammock/matrices/blosum75.txt --- a/v.1.1.0/Hammock/matrices/blosum75.txt Fri Jun 23 05:40:22 2017 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,31 +0,0 @@ -# Matrix made by matblas from blosum75.iij -# * column uses minimum score -# BLOSUM Clustered Scoring Matrix in 1/2 Bit Units -# Blocks Database = /data/blocks_5.0/blocks.dat -# Cluster Percentage: >= 75 -# Entropy = 0.9077, Expected = -0.6845 - A R N D C Q E G H I L K M F P S T W Y V B Z X * -A 4 -2 -2 -2 -1 -1 -1 0 -2 -2 -2 -1 -1 -3 -1 1 0 -3 -2 0 -2 -1 -1 -5 -R -2 6 -1 -2 -4 1 0 -3 0 -3 -3 2 -2 -3 -2 -1 -1 -3 -2 -3 -1 0 -1 -5 -N -2 -1 6 1 -3 0 -1 -1 0 -4 -4 0 -3 -4 -3 0 0 -4 -3 -3 3 0 -1 -5 -D -2 -2 1 6 -4 -1 1 -2 -1 -4 -4 -1 -4 -4 -2 -1 -1 -5 -4 -4 4 1 -2 -5 -C -1 -4 -3 -4 9 -3 -5 -3 -4 -1 -2 -4 -2 -2 -4 -1 -1 -3 -3 -1 -4 -4 -2 -5 -Q -1 1 0 -1 -3 6 2 -2 1 -3 -3 1 0 -4 -2 0 -1 -2 -2 -2 0 3 -1 -5 -E -1 0 -1 1 -5 2 5 -3 0 -4 -4 1 -2 -4 -1 0 -1 -4 -3 -3 1 4 -1 -5 -G 0 -3 -1 -2 -3 -2 -3 6 -2 -5 -4 -2 -3 -4 -3 -1 -2 -3 -4 -4 -1 -2 -2 -5 -H -2 0 0 -1 -4 1 0 -2 8 -4 -3 -1 -2 -2 -2 -1 -2 -2 2 -4 -1 0 -1 -5 -I -2 -3 -4 -4 -1 -3 -4 -5 -4 4 1 -3 1 0 -3 -3 -1 -3 -2 3 -4 -4 -2 -5 -L -2 -3 -4 -4 -2 -3 -4 -4 -3 1 4 -3 2 0 -3 -3 -2 -2 -1 1 -4 -3 -1 -5 -K -1 2 0 -1 -4 1 1 -2 -1 -3 -3 5 -2 -4 -1 0 -1 -4 -2 -3 -1 1 -1 -5 -M -1 -2 -3 -4 -2 0 -2 -3 -2 1 2 -2 6 0 -3 -2 -1 -2 -2 1 -3 -2 -1 -5 -F -3 -3 -4 -4 -2 -4 -4 -4 -2 0 0 -4 0 6 -4 -3 -2 1 3 -1 -4 -4 -2 -5 -P -1 -2 -3 -2 -4 -2 -1 -3 -2 -3 -3 -1 -3 -4 8 -1 -1 -5 -4 -3 -2 -2 -2 -5 -S 1 -1 0 -1 -1 0 0 -1 -1 -3 -3 0 -2 -3 -1 5 1 -3 -2 -2 0 0 -1 -5 -T 0 -1 0 -1 -1 -1 -1 -2 -2 -1 -2 -1 -1 -2 -1 1 5 -3 -2 0 -1 -1 -1 -5 -W -3 -3 -4 -5 -3 -2 -4 -3 -2 -3 -2 -4 -2 1 -5 -3 -3 11 2 -3 -5 -3 -3 -5 -Y -2 -2 -3 -4 -3 -2 -3 -4 2 -2 -1 -2 -2 3 -4 -2 -2 2 7 -2 -3 -3 -2 -5 -V 0 -3 -3 -4 -1 -2 -3 -4 -4 3 1 -3 1 -1 -3 -2 0 -3 -2 4 -4 -3 -1 -5 -B -2 -1 3 4 -4 0 1 -1 -1 -4 -4 -1 -3 -4 -2 0 -1 -5 -3 -4 4 0 -2 -5 -Z -1 0 0 1 -4 3 4 -2 0 -4 -3 1 -2 -4 -2 0 -1 -3 -3 -3 0 4 -1 -5 -X -1 -1 -1 -2 -2 -1 -1 -2 -1 -2 -1 -1 -1 -2 -2 -1 -1 -3 -2 -1 -2 -1 -1 -5 -* -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 1 |
| b |
| diff -r 7950e4c52972 -r 22b245c1bb94 v.1.1.0/Hammock/matrices/blosum80.txt --- a/v.1.1.0/Hammock/matrices/blosum80.txt Fri Jun 23 05:40:22 2017 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,31 +0,0 @@ -# Matrix made by matblas from blosum80_3.iij -# * column uses minimum score -# BLOSUM Clustered Scoring Matrix in 1/3 Bit Units -# Blocks Database = /data/blocks_5.0/blocks.dat -# Cluster Percentage: >= 80 -# Entropy = 0.9868, Expected = -0.7442 - A R N D C Q E G H I L K M F P S T W Y V B Z X * -A 7 -3 -3 -3 -1 -2 -2 0 -3 -3 -3 -1 -2 -4 -1 2 0 -5 -4 -1 -3 -2 -1 -8 -R -3 9 -1 -3 -6 1 -1 -4 0 -5 -4 3 -3 -5 -3 -2 -2 -5 -4 -4 -2 0 -2 -8 -N -3 -1 9 2 -5 0 -1 -1 1 -6 -6 0 -4 -6 -4 1 0 -7 -4 -5 5 -1 -2 -8 -D -3 -3 2 10 -7 -1 2 -3 -2 -7 -7 -2 -6 -6 -3 -1 -2 -8 -6 -6 6 1 -3 -8 -C -1 -6 -5 -7 13 -5 -7 -6 -7 -2 -3 -6 -3 -4 -6 -2 -2 -5 -5 -2 -6 -7 -4 -8 -Q -2 1 0 -1 -5 9 3 -4 1 -5 -4 2 -1 -5 -3 -1 -1 -4 -3 -4 -1 5 -2 -8 -E -2 -1 -1 2 -7 3 8 -4 0 -6 -6 1 -4 -6 -2 -1 -2 -6 -5 -4 1 6 -2 -8 -G 0 -4 -1 -3 -6 -4 -4 9 -4 -7 -7 -3 -5 -6 -5 -1 -3 -6 -6 -6 -2 -4 -3 -8 -H -3 0 1 -2 -7 1 0 -4 12 -6 -5 -1 -4 -2 -4 -2 -3 -4 3 -5 -1 0 -2 -8 -I -3 -5 -6 -7 -2 -5 -6 -7 -6 7 2 -5 2 -1 -5 -4 -2 -5 -3 4 -6 -6 -2 -8 -L -3 -4 -6 -7 -3 -4 -6 -7 -5 2 6 -4 3 0 -5 -4 -3 -4 -2 1 -7 -5 -2 -8 -K -1 3 0 -2 -6 2 1 -3 -1 -5 -4 8 -3 -5 -2 -1 -1 -6 -4 -4 -1 1 -2 -8 -M -2 -3 -4 -6 -3 -1 -4 -5 -4 2 3 -3 9 0 -4 -3 -1 -3 -3 1 -5 -3 -2 -8 -F -4 -5 -6 -6 -4 -5 -6 -6 -2 -1 0 -5 0 10 -6 -4 -4 0 4 -2 -6 -6 -3 -8 -P -1 -3 -4 -3 -6 -3 -2 -5 -4 -5 -5 -2 -4 -6 12 -2 -3 -7 -6 -4 -4 -2 -3 -8 -S 2 -2 1 -1 -2 -1 -1 -1 -2 -4 -4 -1 -3 -4 -2 7 2 -6 -3 -3 0 -1 -1 -8 -T 0 -2 0 -2 -2 -1 -2 -3 -3 -2 -3 -1 -1 -4 -3 2 8 -5 -3 0 -1 -2 -1 -8 -W -5 -5 -7 -8 -5 -4 -6 -6 -4 -5 -4 -6 -3 0 -7 -6 -5 16 3 -5 -8 -5 -5 -8 -Y -4 -4 -4 -6 -5 -3 -5 -6 3 -3 -2 -4 -3 4 -6 -3 -3 3 11 -3 -5 -4 -3 -8 -V -1 -4 -5 -6 -2 -4 -4 -6 -5 4 1 -4 1 -2 -4 -3 0 -5 -3 7 -6 -4 -2 -8 -B -3 -2 5 6 -6 -1 1 -2 -1 -6 -7 -1 -5 -6 -4 0 -1 -8 -5 -6 6 0 -3 -8 -Z -2 0 -1 1 -7 5 6 -4 0 -6 -5 1 -3 -6 -2 -1 -2 -5 -4 -4 0 6 -1 -8 -X -1 -2 -2 -3 -4 -2 -2 -3 -2 -2 -2 -2 -2 -3 -3 -1 -1 -5 -3 -2 -3 -1 -2 -8 -* -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 1 |
| b |
| diff -r 7950e4c52972 -r 22b245c1bb94 v.1.1.0/Hammock/matrices/blosum85.txt --- a/v.1.1.0/Hammock/matrices/blosum85.txt Fri Jun 23 05:40:22 2017 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,31 +0,0 @@ -# Matrix made by matblas from blosum85.iij -# * column uses minimum score -# BLOSUM Clustered Scoring Matrix in 1/2 Bit Units -# Blocks Database = /data/blocks_5.0/blocks.dat -# Cluster Percentage: >= 85 -# Entropy = 1.0805, Expected = -0.8153 - A R N D C Q E G H I L K M F P S T W Y V B Z X * -A 5 -2 -2 -2 -1 -1 -1 0 -2 -2 -2 -1 -2 -3 -1 1 0 -3 -3 -1 -2 -1 -1 -6 -R -2 6 -1 -2 -4 1 -1 -3 0 -4 -3 2 -2 -4 -2 -1 -2 -4 -3 -3 -2 0 -2 -6 -N -2 -1 7 1 -4 0 -1 -1 0 -4 -4 0 -3 -4 -3 0 0 -5 -3 -4 4 -1 -2 -6 -D -2 -2 1 7 -5 -1 1 -2 -2 -5 -5 -1 -4 -4 -2 -1 -2 -6 -4 -4 4 1 -2 -6 -C -1 -4 -4 -5 9 -4 -5 -4 -5 -2 -2 -4 -2 -3 -4 -2 -2 -4 -3 -1 -4 -5 -3 -6 -Q -1 1 0 -1 -4 6 2 -3 1 -4 -3 1 0 -4 -2 -1 -1 -3 -2 -3 -1 4 -1 -6 -E -1 -1 -1 1 -5 2 6 -3 -1 -4 -4 0 -3 -4 -2 -1 -1 -4 -4 -3 0 4 -1 -6 -G 0 -3 -1 -2 -4 -3 -3 6 -3 -5 -5 -2 -4 -4 -3 -1 -2 -4 -5 -4 -1 -3 -2 -6 -H -2 0 0 -2 -5 1 -1 -3 8 -4 -3 -1 -3 -2 -3 -1 -2 -3 2 -4 -1 0 -2 -6 -I -2 -4 -4 -5 -2 -4 -4 -5 -4 5 1 -3 1 -1 -4 -3 -1 -3 -2 3 -5 -4 -2 -6 -L -2 -3 -4 -5 -2 -3 -4 -5 -3 1 4 -3 2 0 -4 -3 -2 -3 -2 0 -5 -4 -2 -6 -K -1 2 0 -1 -4 1 0 -2 -1 -3 -3 6 -2 -4 -2 -1 -1 -5 -3 -3 -1 1 -1 -6 -M -2 -2 -3 -4 -2 0 -3 -4 -3 1 2 -2 7 -1 -3 -2 -1 -2 -2 0 -4 -2 -1 -6 -F -3 -4 -4 -4 -3 -4 -4 -4 -2 -1 0 -4 -1 7 -4 -3 -3 0 3 -1 -4 -4 -2 -6 -P -1 -2 -3 -2 -4 -2 -2 -3 -3 -4 -4 -2 -3 -4 8 -1 -2 -5 -4 -3 -3 -2 -2 -6 -S 1 -1 0 -1 -2 -1 -1 -1 -1 -3 -3 -1 -2 -3 -1 5 1 -4 -2 -2 0 -1 -1 -6 -T 0 -2 0 -2 -2 -1 -1 -2 -2 -1 -2 -1 -1 -3 -2 1 5 -4 -2 0 -1 -1 -1 -6 -W -3 -4 -5 -6 -4 -3 -4 -4 -3 -3 -3 -5 -2 0 -5 -4 -4 11 2 -3 -5 -4 -3 -6 -Y -3 -3 -3 -4 -3 -2 -4 -5 2 -2 -2 -3 -2 3 -4 -2 -2 2 7 -2 -4 -3 -2 -6 -V -1 -3 -4 -4 -1 -3 -3 -4 -4 3 0 -3 0 -1 -3 -2 0 -3 -2 5 -4 -3 -1 -6 -B -2 -2 4 4 -4 -1 0 -1 -1 -5 -5 -1 -4 -4 -3 0 -1 -5 -4 -4 4 0 -2 -6 -Z -1 0 -1 1 -5 4 4 -3 0 -4 -4 1 -2 -4 -2 -1 -1 -4 -3 -3 0 4 -1 -6 -X -1 -2 -2 -2 -3 -1 -1 -2 -2 -2 -2 -1 -1 -2 -2 -1 -1 -3 -2 -1 -2 -1 -2 -6 -* -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 1 |
| b |
| diff -r 7950e4c52972 -r 22b245c1bb94 v.1.1.0/Hammock/matrices/blosum90.txt --- a/v.1.1.0/Hammock/matrices/blosum90.txt Fri Jun 23 05:40:22 2017 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,31 +0,0 @@ -# Matrix made by matblas from blosum90.iij -# * column uses minimum score -# BLOSUM Clustered Scoring Matrix in 1/2 Bit Units -# Blocks Database = /data/blocks_5.0/blocks.dat -# Cluster Percentage: >= 90 -# Entropy = 1.1806, Expected = -0.8887 - A R N D C Q E G H I L K M F P S T W Y V B Z X * -A 5 -2 -2 -3 -1 -1 -1 0 -2 -2 -2 -1 -2 -3 -1 1 0 -4 -3 -1 -2 -1 -1 -6 -R -2 6 -1 -3 -5 1 -1 -3 0 -4 -3 2 -2 -4 -3 -1 -2 -4 -3 -3 -2 0 -2 -6 -N -2 -1 7 1 -4 0 -1 -1 0 -4 -4 0 -3 -4 -3 0 0 -5 -3 -4 4 -1 -2 -6 -D -3 -3 1 7 -5 -1 1 -2 -2 -5 -5 -1 -4 -5 -3 -1 -2 -6 -4 -5 4 0 -2 -6 -C -1 -5 -4 -5 9 -4 -6 -4 -5 -2 -2 -4 -2 -3 -4 -2 -2 -4 -4 -2 -4 -5 -3 -6 -Q -1 1 0 -1 -4 7 2 -3 1 -4 -3 1 0 -4 -2 -1 -1 -3 -3 -3 -1 4 -1 -6 -E -1 -1 -1 1 -6 2 6 -3 -1 -4 -4 0 -3 -5 -2 -1 -1 -5 -4 -3 0 4 -2 -6 -G 0 -3 -1 -2 -4 -3 -3 6 -3 -5 -5 -2 -4 -5 -3 -1 -3 -4 -5 -5 -2 -3 -2 -6 -H -2 0 0 -2 -5 1 -1 -3 8 -4 -4 -1 -3 -2 -3 -2 -2 -3 1 -4 -1 0 -2 -6 -I -2 -4 -4 -5 -2 -4 -4 -5 -4 5 1 -4 1 -1 -4 -3 -1 -4 -2 3 -5 -4 -2 -6 -L -2 -3 -4 -5 -2 -3 -4 -5 -4 1 5 -3 2 0 -4 -3 -2 -3 -2 0 -5 -4 -2 -6 -K -1 2 0 -1 -4 1 0 -2 -1 -4 -3 6 -2 -4 -2 -1 -1 -5 -3 -3 -1 1 -1 -6 -M -2 -2 -3 -4 -2 0 -3 -4 -3 1 2 -2 7 -1 -3 -2 -1 -2 -2 0 -4 -2 -1 -6 -F -3 -4 -4 -5 -3 -4 -5 -5 -2 -1 0 -4 -1 7 -4 -3 -3 0 3 -2 -4 -4 -2 -6 -P -1 -3 -3 -3 -4 -2 -2 -3 -3 -4 -4 -2 -3 -4 8 -2 -2 -5 -4 -3 -3 -2 -2 -6 -S 1 -1 0 -1 -2 -1 -1 -1 -2 -3 -3 -1 -2 -3 -2 5 1 -4 -3 -2 0 -1 -1 -6 -T 0 -2 0 -2 -2 -1 -1 -3 -2 -1 -2 -1 -1 -3 -2 1 6 -4 -2 -1 -1 -1 -1 -6 -W -4 -4 -5 -6 -4 -3 -5 -4 -3 -4 -3 -5 -2 0 -5 -4 -4 11 2 -3 -6 -4 -3 -6 -Y -3 -3 -3 -4 -4 -3 -4 -5 1 -2 -2 -3 -2 3 -4 -3 -2 2 8 -3 -4 -3 -2 -6 -V -1 -3 -4 -5 -2 -3 -3 -5 -4 3 0 -3 0 -2 -3 -2 -1 -3 -3 5 -4 -3 -2 -6 -B -2 -2 4 4 -4 -1 0 -2 -1 -5 -5 -1 -4 -4 -3 0 -1 -6 -4 -4 4 0 -2 -6 -Z -1 0 -1 0 -5 4 4 -3 0 -4 -4 1 -2 -4 -2 -1 -1 -4 -3 -3 0 4 -1 -6 -X -1 -2 -2 -2 -3 -1 -2 -2 -2 -2 -2 -1 -1 -2 -2 -1 -1 -3 -2 -2 -2 -1 -2 -6 -* -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 1 |
| b |
| diff -r 7950e4c52972 -r 22b245c1bb94 v.1.1.0/Hammock/matrices/gonnet250.txt --- a/v.1.1.0/Hammock/matrices/gonnet250.txt Fri Jun 23 05:40:22 2017 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,26 +0,0 @@ -# PAM 250 matrix recommended by Gonnet, Cohen & Benner -# Science June 5, 1992. -# Values rounded to nearest integer - C S T P A G N D E Q H R K M I L V F Y W X * -C 12 0 0 -3 0 -2 -2 -3 -3 -2 -1 -2 -3 -1 -1 -2 0 -1 0 -1 -3 -8 -S 0 2 2 0 1 0 1 0 0 0 0 0 0 -1 -2 -2 -1 -3 -2 -3 0 -8 -T 0 2 2 0 1 -1 0 0 0 0 0 0 0 -1 -1 -1 0 -2 -2 -4 0 -8 -P -3 0 0 8 0 -2 -1 -1 0 0 -1 -1 -1 -2 -3 -2 -2 -4 -3 -5 -1 -8 -A 0 1 1 0 2 0 0 0 0 0 -1 -1 0 -1 -1 -1 0 -2 -2 -4 0 -8 -G -2 0 -1 -2 0 7 0 0 -1 -1 -1 -1 -1 -4 -4 -4 -3 -5 -4 -4 -1 -8 -N -2 1 0 -1 0 0 4 2 1 1 1 0 1 -2 -3 -3 -2 -3 -1 -4 0 -8 -D -3 0 0 -1 0 0 2 5 3 1 0 0 0 -3 -4 -4 -3 -4 -3 -5 -1 -8 -E -3 0 0 0 0 -1 1 3 4 2 0 0 1 -2 -3 -3 -2 -4 -3 -4 -1 -8 -Q -2 0 0 0 0 -1 1 1 2 3 1 2 2 -1 -2 -2 -2 -3 -2 -3 -1 -8 -H -1 0 0 -1 -1 -1 1 0 0 1 6 1 1 -1 -2 -2 -2 0 2 -1 -1 -8 -R -2 0 0 -1 -1 -1 0 0 0 2 1 5 3 -2 -2 -2 -2 -3 -2 -2 -1 -8 -K -3 0 0 -1 0 -1 1 0 1 2 1 3 3 -1 -2 -2 -2 -3 -2 -4 -1 -8 -M -1 -1 -1 -2 -1 -4 -2 -3 -2 -1 -1 -2 -1 4 2 3 2 2 0 -1 -1 -8 -I -1 -2 -1 -3 -1 -4 -3 -4 -3 -2 -2 -2 -2 2 4 3 3 1 -1 -2 -1 -8 -L -2 -2 -1 -2 -1 -4 -3 -4 -3 -2 -2 -2 -2 3 3 4 2 2 0 -1 -1 -8 -V 0 -1 0 -2 0 -3 -2 -3 -2 -2 -2 -2 -2 2 3 2 3 0 -1 -3 -1 -8 -F -1 -3 -2 -4 -2 -5 -3 -4 -4 -3 0 -3 -3 2 1 2 0 7 5 4 -2 -8 -Y 0 -2 -2 -3 -2 -4 -1 -3 -3 -2 2 -2 -2 0 -1 0 -1 5 8 4 -2 -8 -W -1 -3 -4 -5 -4 -4 -4 -5 -4 -3 -1 -2 -4 -1 -2 -1 -3 4 4 14 -4 -8 -X -3 0 0 -1 0 -1 0 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -2 -2 -4 -1 -8 -* -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 1 |
| b |
| diff -r 7950e4c52972 -r 22b245c1bb94 v.1.1.0/Hammock/matrices/mcla71.txt --- a/v.1.1.0/Hammock/matrices/mcla71.txt Fri Jun 23 05:40:22 2017 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,22 +0,0 @@ -# McLachlan 1971 - A R N D C Q E G H I L K M F P S T W Y V -A 8 2 3 3 1 3 4 3 3 2 2 3 3 1 4 4 3 1 1 3 -R 2 8 3 1 1 5 3 3 5 1 2 5 1 1 3 4 3 3 2 2 -N 3 3 8 5 1 4 4 3 4 1 1 4 2 0 1 5 3 0 2 1 -D 3 1 5 8 1 4 5 3 4 0 1 3 2 1 3 3 3 0 1 1 -C 1 1 1 1 9 0 0 1 3 1 0 0 3 0 0 2 2 2 1 1 -Q 3 5 4 4 0 8 5 2 4 0 3 4 3 0 3 4 3 2 1 2 -E 4 3 4 5 0 5 8 3 2 1 1 4 1 0 4 4 4 1 2 2 -G 3 3 3 3 1 2 3 8 2 1 1 3 1 0 3 3 2 1 0 2 -H 3 5 4 4 3 4 2 2 8 2 2 4 3 4 3 3 4 3 4 2 -I 2 1 1 0 1 0 1 1 2 8 5 1 5 3 1 2 3 3 3 5 -L 2 2 1 1 0 3 1 1 2 5 8 2 6 5 1 2 3 3 3 5 -K 3 5 4 3 0 4 4 3 4 1 2 8 1 0 3 3 3 1 1 2 -M 3 1 2 2 3 3 1 1 3 5 6 1 8 5 1 2 3 1 2 4 -F 1 1 0 1 0 0 0 0 4 3 5 0 5 9 1 2 1 6 6 3 -P 4 3 1 3 0 3 4 3 3 1 1 3 1 1 8 3 3 0 0 2 -S 4 4 5 3 2 4 4 3 3 2 2 3 2 2 3 8 5 3 3 2 -T 3 3 3 3 2 3 4 2 4 3 3 3 3 1 3 5 8 2 1 3 -W 1 3 0 0 2 2 1 1 3 3 3 1 1 6 0 3 2 9 6 2 -Y 1 2 2 1 1 1 2 0 4 3 3 1 2 6 0 3 1 6 9 3 -V 3 2 1 1 1 2 2 2 2 5 5 2 4 3 2 2 3 2 3 8 |
| b |
| diff -r 7950e4c52972 -r 22b245c1bb94 v.1.1.0/Hammock/matrices/pam250.txt --- a/v.1.1.0/Hammock/matrices/pam250.txt Fri Jun 23 05:40:22 2017 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| @@ -1,34 +0,0 @@ -# -# This matrix was produced by "pam" Version 1.0.6 [28-Jul-93] -# -# PAM 250 substitution matrix, scale = ln(2)/3 = 0.231049 -# -# Expected score = -0.844, Entropy = 0.354 bits -# -# Lowest score = -8, Highest score = 17 -# - A R N D C Q E G H I L K M F P S T W Y V B Z X * -A 2 -2 0 0 -2 0 0 1 -1 -1 -2 -1 -1 -3 1 1 1 -6 -3 0 0 0 0 -8 -R -2 6 0 -1 -4 1 -1 -3 2 -2 -3 3 0 -4 0 0 -1 2 -4 -2 -1 0 -1 -8 -N 0 0 2 2 -4 1 1 0 2 -2 -3 1 -2 -3 0 1 0 -4 -2 -2 2 1 0 -8 -D 0 -1 2 4 -5 2 3 1 1 -2 -4 0 -3 -6 -1 0 0 -7 -4 -2 3 3 -1 -8 -C -2 -4 -4 -5 12 -5 -5 -3 -3 -2 -6 -5 -5 -4 -3 0 -2 -8 0 -2 -4 -5 -3 -8 -Q 0 1 1 2 -5 4 2 -1 3 -2 -2 1 -1 -5 0 -1 -1 -5 -4 -2 1 3 -1 -8 -E 0 -1 1 3 -5 2 4 0 1 -2 -3 0 -2 -5 -1 0 0 -7 -4 -2 3 3 -1 -8 -G 1 -3 0 1 -3 -1 0 5 -2 -3 -4 -2 -3 -5 0 1 0 -7 -5 -1 0 0 -1 -8 -H -1 2 2 1 -3 3 1 -2 6 -2 -2 0 -2 -2 0 -1 -1 -3 0 -2 1 2 -1 -8 -I -1 -2 -2 -2 -2 -2 -2 -3 -2 5 2 -2 2 1 -2 -1 0 -5 -1 4 -2 -2 -1 -8 -L -2 -3 -3 -4 -6 -2 -3 -4 -2 2 6 -3 4 2 -3 -3 -2 -2 -1 2 -3 -3 -1 -8 -K -1 3 1 0 -5 1 0 -2 0 -2 -3 5 0 -5 -1 0 0 -3 -4 -2 1 0 -1 -8 -M -1 0 -2 -3 -5 -1 -2 -3 -2 2 4 0 6 0 -2 -2 -1 -4 -2 2 -2 -2 -1 -8 -F -3 -4 -3 -6 -4 -5 -5 -5 -2 1 2 -5 0 9 -5 -3 -3 0 7 -1 -4 -5 -2 -8 -P 1 0 0 -1 -3 0 -1 0 0 -2 -3 -1 -2 -5 6 1 0 -6 -5 -1 -1 0 -1 -8 -S 1 0 1 0 0 -1 0 1 -1 -1 -3 0 -2 -3 1 2 1 -2 -3 -1 0 0 0 -8 -T 1 -1 0 0 -2 -1 0 0 -1 0 -2 0 -1 -3 0 1 3 -5 -3 0 0 -1 0 -8 -W -6 2 -4 -7 -8 -5 -7 -7 -3 -5 -2 -3 -4 0 -6 -2 -5 17 0 -6 -5 -6 -4 -8 -Y -3 -4 -2 -4 0 -4 -4 -5 0 -1 -1 -4 -2 7 -5 -3 -3 0 10 -2 -3 -4 -2 -8 -V 0 -2 -2 -2 -2 -2 -2 -1 -2 4 2 -2 2 -1 -1 -1 0 -6 -2 4 -2 -2 -1 -8 -B 0 -1 2 3 -4 1 3 0 1 -2 -3 1 -2 -4 -1 0 0 -5 -3 -2 3 2 -1 -8 -Z 0 0 1 3 -5 3 3 0 2 -2 -3 0 -2 -5 0 0 -1 -6 -4 -2 2 3 -1 -8 -X 0 -1 0 -1 -3 -1 -1 -1 -1 -1 -1 -1 -1 -2 -1 0 0 -4 -2 -1 -1 -1 -1 -8 -* -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 1 |
| b |
| diff -r 7950e4c52972 -r 22b245c1bb94 v.1.1.0/Hammock/settings/misc/blosum62.freq_rownorm --- a/v.1.1.0/Hammock/settings/misc/blosum62.freq_rownorm Fri Jun 23 05:40:22 2017 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,25 +0,0 @@ -# BLOSUM Clustered Target Frequencies=qij -# Blocks Database = /data/blocks_5.0/blocks.dat -# Cluster Percentage: >= 62 -# Normalized frequencies (by row) from file: blosum62.qij -A R N D C Q E G H I L K M F P S T W Y V -0.2901 0.0310 0.0256 0.0297 0.0216 0.0256 0.0405 0.0783 0.0148 0.0432 0.0594 0.0445 0.0175 0.0216 0.0297 0.0850 0.0499 0.0054 0.0175 0.0688 -0.0446 0.3450 0.0388 0.0310 0.0078 0.0484 0.0523 0.0329 0.0233 0.0233 0.0465 0.1202 0.0155 0.0174 0.0194 0.0446 0.0349 0.0058 0.0174 0.0310 -0.0427 0.0449 0.3169 0.0831 0.0090 0.0337 0.0494 0.0652 0.0315 0.0225 0.0315 0.0539 0.0112 0.0180 0.0202 0.0697 0.0494 0.0045 0.0157 0.0270 -0.0410 0.0299 0.0690 0.3974 0.0075 0.0299 0.0914 0.0466 0.0187 0.0224 0.0280 0.0448 0.0093 0.0149 0.0224 0.0522 0.0354 0.0037 0.0112 0.0243 -0.0650 0.0163 0.0163 0.0163 0.4837 0.0122 0.0163 0.0325 0.0081 0.0447 0.0650 0.0203 0.0163 0.0203 0.0163 0.0407 0.0366 0.0041 0.0122 0.0569 -0.0559 0.0735 0.0441 0.0471 0.0088 0.2147 0.1029 0.0412 0.0294 0.0265 0.0471 0.0912 0.0206 0.0147 0.0235 0.0559 0.0412 0.0059 0.0206 0.0353 -0.0552 0.0497 0.0405 0.0902 0.0074 0.0645 0.2965 0.0350 0.0258 0.0221 0.0368 0.0755 0.0129 0.0166 0.0258 0.0552 0.0368 0.0055 0.0166 0.0313 -0.0783 0.0229 0.0391 0.0337 0.0108 0.0189 0.0256 0.5101 0.0135 0.0189 0.0283 0.0337 0.0094 0.0162 0.0189 0.0513 0.0297 0.0054 0.0108 0.0243 -0.0420 0.0458 0.0534 0.0382 0.0076 0.0382 0.0534 0.0382 0.3550 0.0229 0.0382 0.0458 0.0153 0.0305 0.0191 0.0420 0.0267 0.0076 0.0573 0.0229 -0.0471 0.0177 0.0147 0.0177 0.0162 0.0133 0.0177 0.0206 0.0088 0.2710 0.1679 0.0236 0.0368 0.0442 0.0147 0.0250 0.0398 0.0059 0.0206 0.1767 -0.0445 0.0243 0.0142 0.0152 0.0162 0.0162 0.0202 0.0213 0.0101 0.1154 0.3755 0.0253 0.0496 0.0547 0.0142 0.0243 0.0334 0.0071 0.0223 0.0962 -0.0570 0.1071 0.0415 0.0415 0.0086 0.0535 0.0708 0.0432 0.0207 0.0276 0.0432 0.2781 0.0155 0.0155 0.0276 0.0535 0.0397 0.0052 0.0173 0.0328 -0.0522 0.0321 0.0201 0.0201 0.0161 0.0281 0.0281 0.0281 0.0161 0.1004 0.1968 0.0361 0.1606 0.0482 0.0161 0.0361 0.0402 0.0080 0.0241 0.0924 -0.0338 0.0190 0.0169 0.0169 0.0106 0.0106 0.0190 0.0254 0.0169 0.0634 0.1142 0.0190 0.0254 0.3869 0.0106 0.0254 0.0254 0.0169 0.0888 0.0550 -0.0568 0.0258 0.0233 0.0310 0.0103 0.0207 0.0362 0.0362 0.0129 0.0258 0.0362 0.0413 0.0103 0.0129 0.4935 0.0439 0.0362 0.0026 0.0129 0.0310 -0.1099 0.0401 0.0541 0.0489 0.0175 0.0332 0.0524 0.0663 0.0192 0.0297 0.0419 0.0541 0.0157 0.0209 0.0297 0.2199 0.0820 0.0052 0.0175 0.0419 -0.0730 0.0355 0.0434 0.0375 0.0178 0.0276 0.0394 0.0434 0.0138 0.0533 0.0651 0.0454 0.0197 0.0237 0.0276 0.0927 0.2465 0.0059 0.0178 0.0710 -0.0303 0.0227 0.0152 0.0152 0.0076 0.0152 0.0227 0.0303 0.0152 0.0303 0.0530 0.0227 0.0152 0.0606 0.0076 0.0227 0.0227 0.4924 0.0682 0.0303 -0.0405 0.0280 0.0218 0.0187 0.0093 0.0218 0.0280 0.0249 0.0467 0.0436 0.0685 0.0312 0.0187 0.1308 0.0156 0.0312 0.0280 0.0280 0.3178 0.0467 -0.0700 0.0219 0.0165 0.0178 0.0192 0.0165 0.0233 0.0247 0.0082 0.1646 0.1303 0.0261 0.0316 0.0357 0.0165 0.0329 0.0494 0.0055 0.0206 0.2689 |
| b |
| diff -r 7950e4c52972 -r 22b245c1bb94 v.1.1.0/Hammock/settings/settings.prop --- a/v.1.1.0/Hammock/settings/settings.prop Fri Jun 23 05:40:22 2017 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| @@ -1,25 +0,0 @@ -#Lines starting with hash (#) are ignored -#Tool commands. Define full paths if needed. By default (not specified) means locations relative to .jar file in Hammock/dist foltder -#clustalOmegaCommand= -#hmmbuildCommand= -#hmmsearchCommand= -#hhmakeCommand= -#hhsearchCommand= -#reformatCommand= -#Directory for all temporal files. Define full path if needed. Default (not specified): /tmp -#tempDirectory= -#Temporal files subdirectories. Define full paths if needed. Default (not specified): directories in tempDirectory/Hammock_temp/[time]/ -#fastaDirectory= -#msaDirectory= -#hmmDirectory= -#hhDirectory= -#hmmsearchOutDirectory= -#hhsearchOutDirectory= -#fastaDatabaseFile= -#Tool parameters. Generally, it is not recommended to change this section. -clustalOmegaParameters= -hmmbuildParameters=--enone --fragthresh 1.0 --hand --wnone --amino --seed 42 -hmmsearchParameters=--nobias --F1 0.5 --F2 0.05 --F3 1e-2 --nonull2 --seed 42 -hmmalignParameters=--outformat selex --amino --seed 42 -hhmakeParameters=-M a2m -id 100 -diff inf -pcm 3 -nocontxt -v 0 -hhsearchParameters=-norealign -alt 1 -corr 0 -shift 0 -ssm 0 -tags -nocons -nopred -nodssp -sc 0 -v 0 -z 2 -Z 500000 -local -p 0.0 -vit -b 100.0 -E 100.0 -e 100.0 -z 100 |
| b |
| diff -r 7950e4c52972 -r 22b245c1bb94 v.1.1.0/Hammock/settings/settings.prop~ --- a/v.1.1.0/Hammock/settings/settings.prop~ Fri Jun 23 05:40:22 2017 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,11 +0,0 @@ -#Change "default" to full path if needed. Default means locations relative to .jar file in PhageClust/dist foltder -#clustalOmegaCommand= -#fastaDirectory= -#msaDirectory= -clustalOmegaParameters=--iter=5 --full-iter -hmmbuildParameters=--enone --fragthresh 1.0 --symfrac 0.6 -hmmsearchParameters=--nobias --F1 0.5 --F2 0.05 --F3 1e-2 -hhmakeParameters=-M a2m -id 100 -qsc -100 -pcm 3 -hhalignParameters=-realign -id 100 -diff inf -alt 1 -corr 0 -shift 0 -ssm 0 -nocontxt -pcm 2 -tags -nocons -nopred -nodssp -M a2m -alt 1 -sc 0 -v 0 -z 2 -Z 20 -local -mact 0.0 -hhsearchParameters=-realign -id 100 -diff inf -alt 1 -corr 0 -shift 0 -ssm 0 -nocontxt -pcm 2 -tags -nocons -nopred -nodssp -M a2m -alt 1 -sc 0 -v 0 -z 2 -Z 500 -local -mact 0.0 -p 0 -reformatParameters=-M 30 |
| b |
| diff -r 7950e4c52972 -r 22b245c1bb94 v.1.1.0/hammock.xml --- a/v.1.1.0/hammock.xml Fri Jun 23 05:40:22 2017 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| b'@@ -1,384 +0,0 @@\n-<tool id="hammock_1.0" name="Hammock - cluster peptides" version="1.1.0" hidden="false">\n-\n- <description>Clusters short peptide sequences</description>\n-\n- <command interpreter="bash">\n-wrapper.sh \\$HAMMOCK_JAR full --galaxy -t \\${GALAXY_SLOTS:-4} -i $input --goc $output_clusters --gos $output_sequences --goo $output_sequences_ordered\n-\n-\t #if $label_params.set_labels == "set":\n- #for $s in $label_params.round_labels:\n-\t\t\t#set $l_field = $l_field + str($s.label) + ","\n-\t\t#end for\t\t\n-\t\t-l $l_field\n-\t #end if\n-\n-\t #if $advanced_initial_params.set_initial_params == "set":\n-\t\t-x $advanced_initial_params.max_shift\n-\t\t-p $advanced_initial_params.shift_penalty\n-\t\t-R $advanced_initial_params.set_order.order\n-\n-\t\t#if $advanced_initial_params.algorithm == "clinkage":\n-\t\t\t--use_clinkage\n-\t\t#end if\n-\n-\t\t#if $advanced_initial_params.algorithm == "greedy":\n-\t\t\t--use_greedy\n-\t\t#end if\n-\n-\t\t#if $advanced_initial_params.set_order.order == "random":\n-\t\t\t-S $advanced_initial_params.set_order.seed\n-\t\t#end if\n-\t\n-\t\t-m \\${MATRIX_PATH}${advanced_initial_params.scoring_matrix}.txt\n- \t#if $advanced_initial_params.initial_params.set_initial == "set":\n- \t-g $advanced_initial_params.initial_params.initial_threshold\n- \t#end if\n- #end if\n-\n- \t #if $advanced_hmm_params.set_hmm_params == "set":\n- \t#if $advanced_hmm_params.threshold_params.clustering_threshold == "part":\n- \t-a $advanced_hmm_params.threshold_params.part_threshold\n- \t#end if\n-\n- \t#if $advanced_hmm_params.threshold_params.clustering_threshold == "size":\n- \t-s $advanced_hmm_params.threshold_params.size_threshold\n- \t#end if\n-\n- \t#if $advanced_hmm_params.threshold_params.clustering_threshold == "count":\n- \t-c $advanced_hmm_params.threshold_params.count_threshold\n- \t#end if\n-\t\t#if $advanced_hmm_params.unique == "unique":\n-\t\t\t--unique\n-\t\t#end if\n-\n-\t \t#set $n_field=""\n-\t \t#set $v_field=""\n-\t \t#set $r_field=""\n-\t\n- \t \t#if $advanced_hmm_params.score_params.set_scores == "set":\n-\t\t\t#if $advanced_hmm_params.score_params.relative_scores == "relative":\n- \t\t-e\n- \t\t#end if\n- \t\t#if $advanced_hmm_params.score_params.relative_scores == "absolute":\n- \t\t-b\n- \t\t#end if\n-\n- \t#for $s in $advanced_hmm_params.score_params.round:\n-\t\t\t\t#set $n_field = $n_field + str($s.assign_score) + ","\n-\t\t\t\t#set $v_field = $v_field + str($s.overlap_score) + ","\n-\t\t\t\t#set $r_field = $r_field + str($s.merge_score) + ","\n-\t\t\t#end for\n-\n-\t\t\t-n $n_field\n-\t\t\t-v $v_field\n-\t\t\t-r $r_field\n- \t#end if\n-\t \t#set $l_field=""\n-\n- \t#if $advanced_hmm_params.match_state_params.set_max_aln_length == "set":\n- \t-j $advanced_hmm_params.match_state_params.max_aln_length\n- \t#end if\n-\n- \t#if $advanced_hmm_params.extension_increase_length == "Yes":\n- \t-q\n- \t#end if\n-\n-\t\t-k $advanced_hmm_params.min_ic \n-\t\t-y $advanced_hmm_params.max_gap_proportion\n-\t\t-u $advanced_hmm_params.max_inner_gaps\n-\t\t-h $advanced_hmm_params.min_match_states\n-\t\t-C $advanced_hmm_params.min_correlation\n-\t#end if\t\t\n-\t\t\t\n-</command>\n-\n- <inputs>\n- <param format="fasta" name="input" type="data" label="Source sequence file" help="File with sequences to cluster in fasta format. See -i, --input in the manual for details." />\n-\n-<conditional name="label_params">\n- <param name="set_labels" type="select" label="Specify a subset of labels to be used" help="Set Automatic to use all labels present in the data or choose a subset of labels to be used. See -l, --labels in the manual for details.">\n- <option value="auto">Automatic - all labels</option>\n- <option value="set">Set list of labels manually</option>\n- </param>\n- <when value="auto" />\n- '..b'package" version="3.1b2">hmmer</requirement>\n-\t\t<requirement type="package" version="2.0.16">hhsuite</requirement>\n- </requirements>\n-\n-\n-<tests>\n- \t<test>\n-\t\t<param name="input" value="input.fa" />\n-\t\t<param name="advanced_initial_params.max_shift" value="3" />\n-\t\t<param name="advanced_initial_params.shift_penalty" value="0" />\n-\t\t<param name="advanced_initial_params.scoring_matrix" value="blosum62" />\n-\t\t<param name="advanced_hmm_params.min_match_states" value="4" />\n-\t\t<param name="advanced_hmm_params.min_ic " value="1.2" />\n-\t\t<param name="advanced_hmm_params.max_gap_proportion" value="0.05" />\n-\t\t<param name="advanced_hmm_params.max_inner_gaps" value="0" />\n-\n-\t\t<output name="output_clusters" file="output_clusters.csv" /> \n-\t\t<output name="output_sequences" file="output_sequences.csv" /> \n-\t</test>\n-</tests>\n-\n-\n-\n-<help>\n-\n-\n-**HAMMOCK version 1.1.0**\n-\n-**Hammock overview**\n-\n-Hammock performs peptide sequence clustering. It is able to identify clusters of sequences sharing a sequence motif within big datasets. For news, documentation and other available versions, see http://www.recamo.cz/en/software/hammock-cluster-peptides/\n-\n-------\n-\n-.. class:: infomark\n-\n-**Citation**\n-Please cite: \n-\n-Krejci, Adam, et al. "Hammock: a hidden Markov model-based peptide clustering algorithm to identify protein-interaction consensus motifs in large datasets." Bioinformatics 32.1 (2016): 9-16.\n-\n-------\n-\n-**Input format**\n-\n-Hammock accepts fasta files. For basic work, fasta description lines (those starting with ">") may contain virtually anything. For work with the concept of sequence labels, description line should be in this form: \n-\n- | >id|count|label\n-\n-an example of two records in this format:\n-\n- | >1|42|label1\n- | RSPIVRQLPSLP\n- | >2|58|label2\n- | GSWVVDISNVED\n-\n-For more detailed description of the label concept and input format, see the documentation_.\n-\n-------\n-\n-**Outputs**\n-\n-Hammock returns three files, all of them are tab-separated tables.\n-\n-The first is the cluster overview file. It contains one line for each resulting cluster plus header. Columns are: \n-\n-cluster_id main_sequence sum label1 label2 label3 ...\n-\n- | cluster_id: Cluster\'s unique numeric identifier.\n- | main_sequence: The most popular (appearing in the highest number of copies) sequence of this cluster\n- | sum: Total count of all sequences in this cluster (sum over all labels)\n- | label1, label2 etc. Counts of sequences with particular labels\n-\n-\n-The second file provides more detailed information. It contains one line for each clustered (unique) sequence plus header. The sequences are ordered according to their presence in clusters, from the largest cluster and within a cluster, from the most abundant sequence.\n-\n-Columns are: \n-\n-cluster_id sequence alignment sum label1 label2 label3 ...\n-\n- | cluster_id: Id of the cluster this sequence belongs to\n- | sequence: Amino acid sequence of this peptide\n- | alignment: Aligned amino acid sequence of this peptide (part of cluster\'s multiple sequence alignment)\n- | sum: Total count of copies of this sequence (sum over all labels)\n- | label1, label2 etc. Counts of copies with particular labels\n-\n-\n-The third file is the same as the second file, with two differences: it also contains sequences not belonging to any cluster (these have "NA" in the cluster_id column) and the order of the sequences in this file is the same as their order in the input fasta file.\n-\n-------\n-\n-**Parameters**\n-Default and auto-detected parameters have been carefully tuned and tested to work well with several datasets, they are especially suited for short peptides from phage display experiments. Neverheless, there is no such thing as universal rules suitable for every dataset - parameter understanding and tuning may be needed. For more detailed description of parameters, see the documentation_.\n-\n-.. _documentation: http://www.recamo.cz/userfiles/file/Software/Hammock/Hammock-manual.pdf\n-\n-\n-</help>\n-\n-</tool>\n' |
| b |
| diff -r 7950e4c52972 -r 22b245c1bb94 v.1.1.0/test-data/input.fa --- a/v.1.1.0/test-data/input.fa Fri Jun 23 05:40:22 2017 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| b'@@ -1,4914 +0,0 @@\n->5006\n-WVTAPRSLPVLP\n->4863\n-GSWVVDISNVED\n->4628\n-NYSGNRPLPGIW\n->6642\n-RSPIVRQLPSLP\n->5810\n-RALPVMPTNGPM\n->4893\n-AKSRPLPMVGLV\n->3919\n-VRPLPSPEGFGQ\n->5831\n-YRGRMLPVIWGT\n->4087\n-RALPLPRAYEGI\n->6358\n-VPLLPIRNGAVN\n->4358\n-PVRVLPNIPLSV\n->6587\n-SYVPGVPLRNLA\n->4003\n-TRVLPNLPVNSQ\n->4836\n-PGLPSRSVSFFN\n->3844\n-RGLPQRPWHSLL\n->3889\n-LAQRPLPLVTAW\n->5804\n-AGQARTLPAIVV\n->5464\n-LAQRPLPLIAAW\n->5401\n-ARASPQVPLGRI\n->4319\n-VSAIIPELPPRG\n->6327\n-RYIPSLPLRNLH\n->4261\n-LRYRTFPNLPEL\n->4429\n-RALPIPNLYMLV\n->4066\n-ARALPQVPSGRI\n->6375\n-KAKFIRELPTVP\n->6631\n-RWVLPELPMNGV\n->5215\n-RKLPTTPNVMSV\n->5970\n-LGPRNRALPIIQ\n->4094\n-RGLPGIPQGIKL\n->6421\n-SGTWALPVPLFG\n->4704\n-IRIHDRNLPVVP\n->6578\n-RTLPVLPTNGPM\n->5433\n-YVRYALPDLPVE\n->4209\n-PPAVPLRGIDLL\n->4784\n-RLRPLPLPMVTL\n->6101\n-RPLPVFPSEVTE\n->5554\n-WWRTPPPKVPFL\n->4184\n-LVAPAIPFRAVE\n->4676\n-RGLPDRPGLGVL\n->3862\n-WTANLFRPLPFV\n->4827\n-GMHLAHRALPLI\n->4405\n-RPLPSIPGLYHV\n->5671\n-ASNLGRLLPPVV\n->5668\n-FRPLPAPAYSFG\n->4304\n-RFYPLLPERNIV\n->4180\n-RALPEVSALSHV\n->4139\n-NYSPMVPALNEL\n->5571\n-GLRALPSFPLGS\n->4582\n-SSALPTRPLAFV\n->5922\n-SGFTRALPSIPP\n->6220\n-YSYKTRGLPAVP\n->5105\n-IWDRQLLMVPVN\n->5935\n-GPPAVPLRDIVV\n->5097\n-LMIPALPDWNWN\n->4422\n-RIAPHLPLMNTW\n->6257\n-RALPEIGNHQTS\n->3750\n-RFERPLPVVGEV\n->5337\n-RSLPAIYLSGDM\n->4649\n-LSVRGLPSIPTQ\n->4873\n-FLATRTLPVPYL\n->5745\n-GIPVVPPRNAVV\n->6513\n-TVLLANRGLPLV\n->6218\n-RPLPVIFNGFSG\n->6207\n-LRYRTVLNLPEL\n->6008\n-SFRGLPSIPWGT\n->3641\n-LRYRELPVTTTV\n->4128\n-LSDIWRIGPNLM\n->5981\n-MRVSASDLPLLP\n->4376\n-FGGNGNRPLPWL\n->4243\n-RGLPSIPTQIFY\n->4797\n-SLAPPLPGMNFV\n->5238\n-LKHRELPFIALD\n->6630\n-QSRALPILPVSD\n->6335\n-VSWVTRKPPFLP\n->4115\n-SVPDVPQRNVIW\n->6048\n-ERWRALPDIPVQ\n->6502\n-LANRALPTTILW\n->4640\n-RQLPRVPLFSDV\n->5225\n-RWWRPLPELASS\n->6510\n-RPLPVISASGFI\n->3648\n-WDRFTRASPLVP\n->5748\n-SHSAMRWLPALL\n->5578\n-GQTDRWLPAVPY\n->5327\n-NVLGRLLPNPGM\n->4342\n-RSLPGPPDAFPW\n->3960\n-YRALPVFPTMSE\n->5117\n-TLAPVVPARNGL\n->3903\n-QVSQDLPPLPYT\n->6290\n-SVWARGLPVSDL\n->4849\n-GYSYGQLPATPW\n->5592\n-WFSARMLPYLPA\n->3738\n-RGPALPLRVLLR\n->6381\n-AHLRALPMPLGA\n->5625\n-KAKLIREMPTVP\n->6239\n-YASVPPVRNQLE\n->4933\n-TDGGRSLPEVPW\n->3721\n-GPGLRGLPSIPV\n->3935\n-VMNGRRLPLLPG\n->5650\n-ARKLPRLPFTQD\n->5224\n-SRSALPLWDVYD\n->5129\n-MPLLPIRNGTVN\n->4681\n-LHQQRALPMAQG\n->4287\n-LMVRALPSIIMH\n->5362\n-KGPLPMIPVRLL\n->4481\n-VRPLPSPEVFGR\n->4742\n-WRSLPAIPTSEF\n->3969\n-GTRALPLVLERF\n->4664\n-IQSRLLPVSPVE\n->6113\n-RARQLPMVPFSQ\n->5548\n-LWLGRTLTSVPS\n->6024\n-ASRRLPSRPVAV\n->4058\n-EGRSLPAVPEFK\n->6085\n-GSQWWKRALPAP\n->5488\n-RPLPRVPGSNAL\n->4106\n-RKLPAVPATEFN\n->6069\n-GNWTKDLPQIVI\n->4176\n-SWVPYLPSRNQL\n->5632\n-RGPLPPIGVDMS\n->4560\n-RALPSAPYNAPY\n->4076\n-SRALLTRPLAFV\n->3832\n-PNWLRPLPGLRE\n->4928\n-RALPVPPGGSVY\n->6485\n-PVGRQLPMIRHI\n->5150\n-LRALPAAPYGAL\n->5077\n-PSSRALPGMPSI\n->3779\n-VPLPLPNASGYG\n->5724\n-SSRRLPLVPTYE\n->3747\n-NEQLFHRPLPAV\n->6060\n-ARPPLPGYNKAM\n->5369\n-LRYRTVPNLPAL\n->3880\n-WTGLQYRILPTG\n->6468\n-GAIPRFLPPIPH\n->4989\n-LRSLPSVPRFGN\n->6192\n-VTWRALPDVPAG\n->5417\n-LYRALPMVYADA\n->6211\n-VPWRALPEVPAG\n->5299\n-LPELPSANFDWN\n->4978\n-LRRRLPAIVELD\n->3775\n-RALPIAPDSIFY\n->5690\n-SRALPTRPLAFA\n->3780\n-GRSLPSLPMGLF\n->4847\n-LHTALPPLPSSM\n->5240\n-TRVSARDLPLLP\n->4579\n-IQSRDLPMVHPY\n->6074\n-FRALPRVPVYVL\n->4783\n-VRKLPKRPTVVI\n->5476\n-SGNTRPLPALSL\n->4456\n-SVARAMMALPGV\n->4132\n-VRVRALPAAPSI\n->5152\n-AMIHERPLPIVG\n->5564\n-LLMQRPLPWEPV\n->5561\n-RTVMISRPLPFP\n->4191\n-RVLPDVPSMQRS\n->4945\n-TRPLPSVIDVSM\n->3817\n-RKLPPTHNVMSV\n->5354\n-RGLPDRPGLGGL\n->3687\n-RWLPSLPHNVPF\n->5450\n-FGPALPARWGGV\n->4597\n-LRSLPSVPWLGN\n->3839\n-QIPSLPLRNQDT\n->6398\n-RLPLKRPLPSLP\n->4590\n-VGRAFRMLPDVT\n->5193\n-FGPRNRALPIIQ\n->3761\n-HAWWRPWTGVLV\n->6058\n-GSWVVDISNVEE\n->6199\n-LSVRGLPNIPSQ\n->3825\n-TVFPGRPLPTPH\n->5976\n-YAPVPPVRNQLK\n->6532\n-VGWSRALPALPS\n->4500\n-VPLLPTRNGTVN\n->5410\n-LWLGRTFPSVPS\n->5301\n-LAMRALPLINLF\n->4956\n-RPLPSVPSAVGL\n->6458\n-LAVRALPLINLL\n->6609\n-SYRALPYAPTVI\n->5973\n-RALPLLPRLAGV\n->5502\n-PPPLPARFRIWT\n->4969\n-RPLPELPERNFL\n->6529\n-VRSLPGVPVFHS\n->4722\n-GVTLLLPARNLY\n->4729\n-RRPLPGLGYMML\n->4329\n-RDLPPFPDAYIV\n->6077\n-GRGLPNIPDVGV\n->4662\n-RARMALPMPYAL\n->6033\n-GPILPPFNSIRQ\n->6137\n-LRIRESPLIEVS\n->3992\n-LMVPAIPDWNWN\n->5856\n-ARSWAQLPTLPI\n->4988\n-GQSGRSLPSVPF\n->6098\n-GGW'..b'DIPLHGVL\n->6161\n-PMRSLPDLPRVV\n->4538\n-GPVLPQRNVAHN\n->4062\n-VLGPPVPPQNVS\n->6096\n-GVALRTRALPVI\n->5712\n-VGVPLPARSLAL\n->6600\n-YSSRIRPLPLVE\n->6607\n-LGGRVLPIPMPV\n->4267\n-WGNGPLPVIPRL\n->3715\n-PGQWAPNLPERY\n->5055\n-GPIVPFRYVLWV\n->5545\n-LGDRPLPSVIGV\n->5277\n-AGPRLPARADVV\n->4754\n-SYRALPVISEAD\n->4679\n-LQYRELPVTTTM\n->5395\n-PGLPGRNIVLIP\n->4472\n-WPGARRLPGLSW\n->4762\n-SHSAMRRLPALW\n->5574\n-LQGRYISLPEIP\n->4769\n-QALPSLPVRYGA\n->5445\n-RALPRIPLQADI\n->4111\n-LGARGLPTIPFH\n->4903\n-DLRPRLPARWGI\n->4118\n-MERALPAVPVDL\n->5272\n-RPLPMIGKTWEI\n->5486\n-RPLPVLEPSEYN\n->5580\n-LRVSSLPVIQML\n->4572\n-FGRALPVLPVVT\n->4546\n-NWNSSRPLPALV\n->5951\n-LRLRSLPVIQML\n->5316\n-QYRALPSAPGYI\n->5739\n-SGLIRWLPTIPG\n->4958\n-VSFLYRRLPMVY\n->5319\n-SMRSLPDLQRVV\n->5543\n-RFERPLPVVGEG\n->5153\n-LPDLPARTHSGF\n->4917\n-LWRRTSLPSLPV\n->4338\n-LSVLGLPNIPTQ\n->5366\n-TYSGSQRALPVV\n->3830\n-GGPMVPPRFLIL\n->6065\n-GPIVPFRDVYVL\n->4612\n-LRYRAVPNLPEL\n->4170\n-KAGLRELPAVVS\n->4017\n-GQISRLPPVLPD\n->6483\n-YDRALPNTPGLD\n->5269\n-VPWRALPDAPAG\n->5253\n-AVFRMLPALPSW\n->3795\n-YVYYYAGLPVVP\n->4913\n-RPVPMPPSFDIT\n->5484\n-ATFGWYALAMEW\n->3770\n-SESRALPEIPYL\n->3725\n-TRRLPGVPQVLL\n->4174\n-FGRSNVLLPAVP\n->6386\n-RSLPKLPGWYSV\n->4785\n-RAGPMLPDRNLH\n->5357\n-AVGPAVDIRWLV\n->5888\n-RKLPPTPNVMSI\n->5053\n-FSVRGLPNIPTQ\n->6197\n-GPVVPYRFLAGF\n->5566\n-GLGQRTLSIIPV\n->6554\n-LPRLPMRVLRAG\n->5978\n-FGRPLPPIVYGQ\n->5197\n-RKLPHTPNVMSV\n->3872\n-RVTSRALPILDV\n->6537\n-YRWRGLPIIAGV\n->3964\n-SRALSWRILPVV\n->5529\n-NRHLPKLPVLVT\n->4378\n-KAKLIRELPTVS\n->5729\n-GPALPARWSLNM\n->5624\n-WWRFFSVDEAIV\n->5007\n-WLNVLRNLPIVP\n->4452\n-NRWRPLPVPHAL\n->5456\n-TRWRILPEVPAS\n->5585\n-RVGRALPDILLS\n->3749\n-VLRPELPSRNMV\n->4469\n-PSSRALPGTPSI\n->6443\n-GQLVLPSIPVDL\n->6277\n-GLRSLPFPPSAL\n->6258\n-GGWRDSALPFTP\n->4563\n-VVNGRRLPLLPG\n->5472\n-RALPVPPGDSVY\n->5264\n-LRYREPPVTTTI\n->3860\n-GQTDRWLSAVPY\n->5307\n-SFFGRTLPVIGS\n->4260\n-VSRALPAMPYGM\n->6362\n-LSDLPARTHSGF\n->4240\n-VRELPRLPLGSL\n->4636\n-RAPLPPVPVLAS\n->3997\n-FGPLSMAPGYAV\n->4592\n-RPLPVPLTDLSL\n->4922\n-SFFGRTLPVIGG\n->4459\n-VYGRALPMAPYR\n->5820\n-TNRDLPSLPDTF\n->4275\n-LFRSRLPMVPYA\n->5693\n-VYGRALPTAPYQ\n->4175\n-RPELPARNQMAV\n->6018\n-RALPVLPTYGPM\n->4055\n-AAMRDLPAWPVS\n->4807\n-FPQLPARYSANV\n->4136\n-RGPLPVTPGYGL\n->5151\n-LHQQRALPMVQG\n->3801\n-PRFRMLPAVLRV\n->4986\n-PSARPLPQYPSY\n->5634\n-RELPFPPVAVVQ\n->5434\n-RPLPLIDRTFGL\n->5026\n-SPPPLPSRGMSI\n->6613\n-RPLPVIAAYNQV\n->5975\n-APRVPMRGYEVN\n->6499\n-HGRSLPARPLLY\n->4677\n-SQVVRALPVVNL\n->6426\n-RGALPSLPGGLY\n->6083\n-RRLPEPGLIAGT\n->3907\n-RALPVPPSDSVY\n->5771\n-LMVPALPDWNWK\n->6524\n-VPSLPIRNGTVN\n->4974\n-RHNGLPQVPGFL\n->5651\n-QVSRDLSPLPYT\n->3691\n-TVPELPERMQIT\n->5673\n-AYRFLPAVPGDQ\n->3650\n-RRTLPDWPLSVY\n->6279\n-VPLLLIRNGTVN\n->4182\n-RSFAPLPLTPHE\n->5461\n-LSRPLPGLPQTL\n->6034\n-PPNLPYRMIKSM\n->5881\n-WRNDSRPLPAIS\n->4265\n-LWLGRTLPSVPR\n->5219\n-VVTGPILPSRLV\n->6318\n-GIRSLPALPGLN\n->6455\n-VATFGPLPSPWT\n->4039\n-RVLPVLPSANQW\n->3703\n-RRSLPIIPINGD\n->5714\n-YYNRRLPDLRVF\n->5778\n-GVGLFRFLPPAP\n->4879\n-RALPPVPLTQIK\n->4894\n-RLELPVRNIMYD\n->5479\n-PRGLLPVAPGWA\n->4697\n-IRPLPPAYNEHI\n->4125\n-ARSAYRILPSIV\n->4559\n-QVSRGLPPLPYT\n->4765\n-KKRPLPAIEHFH\n->3952\n-GQQVLPSIPVDL\n->4371\n-LAVRSLPLINLF\n->4905\n-RLVTYRALPLIM\n->5332\n-RAPELPDRIYVV\n->6296\n-RFDRPLPVVGDV\n->5897\n-RRLPLIPGEMLI\n->4711\n-SRALPTRPLVFV\n->4645\n-SRPTLPARLYYY\n->4404\n-DGAPPLPVWNVV\n->6562\n-GLNVLRNLPFVP\n->3645\n-PPGLPQRSFVAG\n->5602\n-PSERPLPHVPSQ\n->4306\n-TNRLLPNVPGFV\n->6224\n-MRALPVLDVISQ\n->5098\n-RLLPGIPTAMAM\n->4123\n-NRTLPSVPTSNF\n->3959\n-YAGLAYRALPSV\n->6047\n-GRSLPMLPADTR\n->5210\n-RWLPEIPVNMSN\n->3942\n-WRVPSALPPVPI\n->6448\n-DLYAPRGLPLPP\n->6409\n-LSRRLPSILTVQ\n->5746\n-AALAPATPRRAL\n->6583\n-STRPLPALNQMD\n->6370\n-FRRGLPIISSVV\n->6270\n-WSLGGRSLPSLP\n->6102\n-LSVRGLPNIPNQ\n->4700\n-GTANLSRPLPFV\n->4720\n-LMVKALPSIIMQ\n->5926\n-GPRMLPALPTLV\n->3753\n-LRSLPSAPWFGN\n->3894\n-WARRGLPEIPLT\n->4583\n-AAMRDLPARPVS\n->6231\n-PVLSGRNIVLIP\n->6368\n-RLELPARNIMYD\n->4727\n-VRTILDSGLYKS\n->5076\n-GRPLLPVRNLGM\n->4064\n-LPQVPLRNLGAN\n->4162\n-HRWRPLTVPHAL\n->4045\n-MHTRPLPAILFG\n->3922\n-RGLGRALPIVPG\n->5893\n-QRSLPSVPNHTL\n->4746\n-RFSGRPLPMPFQ\n->4877\n-RALWRVLPVEPL\n->5497\n-VPKVPPRFANYL\n->4825\n-PMSLPTVDMTQW\n->6576\n-GAPTLPVRNLLY\n->4197\n-GYRPLPGIPDTE\n->6053\n-NNLYKFRELPVV\n->4366\n-WRSLPAIPTYEL\n->3869\n-VRWRMLPATLGV\n' |
| b |
| diff -r 7950e4c52972 -r 22b245c1bb94 v.1.1.0/test-data/output_clusters.csv --- a/v.1.1.0/test-data/output_clusters.csv Fri Jun 23 05:40:22 2017 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,3 +0,0 @@ -cluster_id;main_sequence;sum;no_label -43;AAMFLRPLPAVQ;1738;1738 -51;AALAPATPRRAL;415;415 |
| b |
| diff -r 7950e4c52972 -r 22b245c1bb94 v.1.1.0/test-data/output_sequences.csv --- a/v.1.1.0/test-data/output_sequences.csv Fri Jun 23 05:40:22 2017 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| b'@@ -1,2154 +0,0 @@\n-cluster_id;sequence;alignment;sum;no_label\n-43;YYYKTRGLPAVP;-YYYKTRGLPAVP------;1;1\n-43;YYNRRLPDLRVF;---YYNRRLPDLRVF----;1;1\n-43;YWPDLPAVPYDQ;----YWPDLPAVPYDQ---;1;1\n-43;YVYYYAGLPVVP;-YVYYYAGLPVVP------;1;1\n-43;YVRYALPDLPVE;---YVRYALPDLPVE----;1;1\n-43;YVRVLPNIPMTK;----YVRVLPNIPMTK---;1;1\n-43;YVALGHRDLPQL;YVALGHRDLPQL-------;1;1\n-43;YTTLSLPSLPNA;---YTTLSLPSLPNA----;1;1\n-43;YTARVLPGIYEF;---YTARVLPGIYEF----;1;1\n-43;YSYKTRGLPAVP;-YSYKTRGLPAVP------;1;1\n-43;YSVRMLPQVPNS;---YSVRMLPQVPNS----;1;1\n-43;YSSRIRPLPLVE;-YSSRIRPLPLVE------;1;1\n-43;YSRPLPFPHSWV;----YSRPLPFPHSWV---;1;1\n-43;YSQRVRALPMFP;-YSQRVRALPMFP------;1;1\n-43;YSQRALPGVSDV;---YSQRALPGVSDV----;1;1\n-43;YSLKGLPLLPRL;---YSLKGLPLLPRL----;1;1\n-43;YSLGRALPSPIL;--YSLGRALPSPIL-----;1;1\n-43;YSGLANRALPSV;YSGLANRALPSV-------;1;1\n-43;YSDRPLPIPAVI;-YSDRPLPIPAVI------;1;1\n-43;YSARTLPGIFHV;---YSARTLPGIFHV----;1;1\n-43;YRWRPLPVPHAL;---YRWRPLPVPHAL----;1;1\n-43;YRWRMLPVIWGT;---YRWRMLPVIWGT----;1;1\n-43;YRWRGLPIIAGV;---YRWRGLPIIAGV----;1;1\n-43;YRWRFLPSLDAL;---YRWRFLPSLDAL----;1;1\n-43;YRWRALPSVSTD;---YRWRALPSVSTD----;1;1\n-43;YRVLPTLPYNMT;-----YRVLPTLPYNMT--;1;1\n-43;YRRPLPSFVQSI;----YRRPLPSFVQSI---;1;1\n-43;YRRELPVIFYEV;----YRRELPVIFYEV---;1;1\n-43;YRPLPTVPRYIE;-----YRPLPTVPRYIE--;1;1\n-43;YRGRMLPVIWGT;---YRGRMLPVIWGT----;1;1\n-43;YRALPVFPTMSE;-----YRALPVFPTMSE--;1;1\n-43;YQSRALPAVWSW;---YQSRALPAVWSW----;1;1\n-43;YNRNLGRELPIL;YNRNLGRELPIL-------;1;1\n-43;YMNWGRALPHPS;-YMNWGRALPHPS------;1;1\n-43;YMFKDVQLPVVP;-YMFKDVQLPVVP------;1;1\n-43;YLPLPGLPFGLV;-----YLPLPGLPFGLV--;1;1\n-43;YLLGFRPLPMVS;-YLLGFRPLPMVS------;1;1\n-43;YLFRALPDVPRN;---YLFRALPDVPRN----;1;1\n-43;YGTRTLPRVILD;---YGTRTLPRVILD----;1;1\n-43;YGRALSGLPSLP;-YGRALSGLPSLP------;1;1\n-43;YGQRPLPLVDGW;---YGQRPLPLVDGW----;1;1\n-43;YGPLPRIPIGYD;-----YGPLPRIPIGYD--;1;1\n-43;YGNPRARMLPII;YGNPRARMLPII-------;1;1\n-43;YGHPTLPAIPVL;---YGHPTLPAIPVL----;1;1\n-43;YGGRLLPLVPVF;---YGGRLLPLVPVF----;1;1\n-43;YGGRLLPLVPGF;---YGGRLLPLVPGF----;1;1\n-43;YGGRLLPDRPNF;---YGGRLLPDRPNF----;1;1\n-43;YGDLAHRALPAV;YGDLAHRALPAV-------;1;1\n-43;YGAGRLLPPLPW;--YGAGRLLPPLPW-----;1;1\n-43;YDRALPNTPGLD;----YDRALPNTPGLD---;1;1\n-43;YDGRFRTLPIPV;-YDGRFRTLPIPV------;1;1\n-43;YARYALPDLPVE;---YARYALPDLPVE----;1;1\n-43;YAIYKLGLPDVP;-YAIYKLGLPDVP------;1;1\n-43;YAGPANRALPSV;YAGPANRALPSV-------;1;1\n-43;YAGMANRALPSV;YAGMANRALPSV-------;1;1\n-43;YAGLAYRALPSV;YAGLAYRALPSV-------;1;1\n-43;YAGLANRALPSV;YAGLANRALPSV-------;1;1\n-43;YAELANRALPSV;YAELANRALPSV-------;1;1\n-43;WYHGLPAVPMYN;----WYHGLPAVPMYN---;1;1\n-43;WWSNRALPMLMV;--WWSNRALPMLMV-----;1;1\n-43;WWRTPLPKVPFM;---WWRTPLPKVPFM----;1;1\n-43;WWRTPLPKVPFL;---WWRTPLPKVPFL----;1;1\n-43;WVVRPLPVVGAF;---WVVRPLPVVGAF----;1;1\n-43;WVTAPRSLPVLP;-WVTAPRSLPVLP------;1;1\n-43;WVRWKELPMVPH;--WVRWKELPMVPH-----;1;1\n-43;WVRPLPELYMIG;----WVRPLPELYMIG---;1;1\n-43;WVRPLPELHMIG;----WVRPLPELHMIG---;1;1\n-43;WVMAPRSLPVLP;-WVMAPRSLPVLP------;1;1\n-43;WVHQLRPLPLPV;-WVHQLRPLPLPV------;1;1\n-43;WVGWKELPMVPH;--WVGWKELPMVPH-----;1;1\n-43;WTVMGRALPVLG;-WTVMGRALPVLG------;1;1\n-43;WTSRTLPSVPFF;---WTSRTLPSVPFF----;1;1\n-43;WTGLRYRILPTV;WTGLRYRILPTV-------;1;1\n-43;WTGLQYRILPTV;WTGLQYRILPTV-------;1;1\n-43;WTGLQYRILPTI;WTGLQYRILPTI-------;1;1\n-43;WTGLQYRILPTG;WTGLQYRILPTG-------;1;1\n-43;WTAVWRSLPIIP;-WTAVWRSLPIIP------;1;1\n-43;WTAVGRSLPVIP;-WTAVGRSLPVIP------;1;1\n-43;WTAVGRSLPIIP;-WTAVGRSLPIIP------;1;1\n-43;WTAVGRSLHIIP;-WTAVGRSLHIIP------;1;1\n-43;WTANLFRPLPFV;WTANLFRPLPFV-------;1;1\n-43;WSYPSRALPRVP;-WSYPSRALPRVP------;1;1\n-43;WSWRALPELWFD;---WSWRALPELWFD----;1;1\n-43;WSSLPAIPTYEF;-----WSSLPAIPTYEF--;1;1\n-43;WSRALPRVPMTD;----WSRALPRVPMTD---;1;1\n-43;WSRALPIIGAGT;----WSRALPIIGAGT---;1;1\n-43;WSQRSLPDIVAY;---WSQRSLPDIVAY----;1;1\n-43;WSLRRALPVEPF;--WSLRRALPVEPF-----;1;1\n-43;WSLHRALPVEPF;--WSLHRALPVEPF-----;1;1\n-43;WSLGGRSLPSLP;-WSLGGRSLPSLP------;1;1\n-43;WSKPMRPLPVML;-WSKPMRPLPVML------;1;1\n-43;WRYLPSPPESAL;-----WRYLPSPPESAL--;1;1\n-43;WRWRALPFVDIA;---WRWRALPFVDIA----;1;1\n-43;WRVPSALPSIPI;--WRVPSALPSIPI-----;1;1\n-43;WRVPSALPPVPI;--WRVPSALPPVPI-----;1;1\n-43;WRVPSALPPIPI;--WRVPSALPPIPI-----;1;1\n'..b'51;GPPAVPLRDIVV;----GPPAVPLRDIVV--;1;1\n-51;GPMLPVWNSVGS;-----GPMLPVWNSVGS-;1;1\n-51;GPLLPVRSVDLL;-----GPLLPVRSVDLL-;1;1\n-51;GPLLPVRSADLL;-----GPLLPVRSADLL-;1;1\n-51;GPLLPPRMAMLK;-----GPLLPPRMAMLK-;1;1\n-51;GPIVPFRYVLWV;-----GPIVPFRYVLWV-;1;1\n-51;GPIVPFRNVYVL;-----GPIVPFRNVYVL-;1;1\n-51;GPIVPFRDVYVL;-----GPIVPFRDVYVL-;1;1\n-51;GPILPPFNSIRQ;-----GPILPPFNSIRQ-;1;1\n-51;GPILPPFNSIGQ;-----GPILPPFNSIGQ-;1;1\n-51;GPILPKREWVSV;-----GPILPKREWVSV-;1;1\n-51;GPFLPVRNSSIW;-----GPFLPVRNSSIW-;1;1\n-51;GPFLPERNVVAV;-----GPFLPERNVVAV-;1;1\n-51;GPELPSRTVYTD;-----GPELPSRTVYTD-;1;1\n-51;GPDVPKRSYIES;-----GPDVPKRSYIES-;1;1\n-51;GPDLPPWVLNLV;-----GPDLPPWVLNLV-;1;1\n-51;GPALPFRVWSDL;-----GPALPFRVWSDL-;1;1\n-51;GPALPFRNSIYV;-----GPALPFRNSIYV-;1;1\n-51;GPALPFRNSIYA;-----GPALPFRNSIYA-;1;1\n-51;GPALPARWSSNM;-----GPALPARWSSNM-;1;1\n-51;GPALPARWSLNM;-----GPALPARWSLNM-;1;1\n-51;GPALPARWSFNM;-----GPALPARWSFNM-;1;1\n-51;GPALPARTVGIL;-----GPALPARTVGIL-;1;1\n-51;GLVLPQRNVAHN;-----GLVLPQRNVAHN-;1;1\n-51;GLQPVLPPRNLV;---GLQPVLPPRNLV---;1;1\n-51;GLQPGLPPRNLV;---GLQPGLPPRNLV---;1;1\n-51;GLPAVPLRDIVV;----GLPAVPLRDIVV--;1;1\n-51;GLELPARNIMYD;-----GLELPARNIMYD-;1;1\n-51;GKPGLPLRPVVL;----GKPGLPLRPVVL--;1;1\n-51;GIPVVPPRNAVV;----GIPVVPPRNAVV--;1;1\n-51;GIPEIPARNWAV;----GIPEIPARNWAV--;1;1\n-51;GIPEIPAGNWAV;----GIPEIPAGNWAV--;1;1\n-51;GGSPELPKRNVW;---GGSPELPKRNVW---;1;1\n-51;GGPMVPPRFWIL;----GGPMVPPRFWIL--;1;1\n-51;GGPMVPPRFLIL;----GGPMVPPRFLIL--;1;1\n-51;GDKPMVPARAFL;---GDKPMVPARAFL---;1;1\n-51;GAPTLPVRNLLY;----GAPTLPVRNLLY--;1;1\n-51;GAPALPDRVSAF;----GAPALPDRVSAF--;1;1\n-51;FVPPLPARNNFI;----FVPPLPARNNFI--;1;1\n-51;FSPSLPIRNAYM;----FSPSLPIRNAYM--;1;1\n-51;FSAPALPARSDW;---FSAPALPARSDW---;1;1\n-51;FRPLLPPRLEGL;----FRPLLPPRLEGL--;1;1\n-51;FRPLLPPRLEEL;----FRPLLPPRLEEL--;1;1\n-51;FPVVPPRNLMGL;-----FPVVPPRNLMGL-;1;1\n-51;FPQLPARYSANV;-----FPQLPARYSANV-;1;1\n-51;FPQLPARYSAIV;-----FPQLPARYSAIV-;1;1\n-51;FPPVPYRSELTL;-----FPPVPYRSELTL-;1;1\n-51;FPILPSRTMAAV;-----FPILPSRTMAAV-;1;1\n-51;FPALPSLNSVFD;-----FPALPSLNSVFD-;1;1\n-51;FMPPLVPARVAL;---FMPPLVPARVAL---;1;1\n-51;FLPWSLPARNSY;---FLPWSLPARNSY---;1;1\n-51;FKGPQLPMANAW;---FKGPQLPMANAW---;1;1\n-51;FGSPRLPPRNLA;---FGSPRLPPRNLA---;1;1\n-51;FGSPRLPPRDLA;---FGSPRLPPRDLA---;1;1\n-51;FGPALPARWGGV;----FGPALPARWGGV--;1;1\n-51;FGGPMLPSWNVF;---FGGPMLPSWNVF---;1;1\n-51;FGGPILPSWNVF;---FGGPILPSWNVF---;1;1\n-51;FAPVLPERNPTM;----FAPVLPERNPTM--;1;1\n-51;EYSPSLPVWNLT;---EYSPSLPVWNLT---;1;1\n-51;EYPNLPARNVYL;----EYPNLPARNVYL--;1;1\n-51;EYGPTLPYRVLL;---EYGPTLPYRVLL---;1;1\n-51;ERPLLPVRNLGI;----ERPLLPVRNLGI--;1;1\n-51;ELSPPVPTRYYM;---ELSPPVPTRYYM---;1;1\n-51;DVAPALPVRLAV;---DVAPALPVRLAV---;1;1\n-51;DLRPRLPARWVI;---DLRPRLPARWVI---;1;1\n-51;DLRPRLPARWMI;---DLRPRLPARWMI---;1;1\n-51;DLRPRLPARWGI;---DLRPRLPARWGI---;1;1\n-51;DLGPLLPSRNVS;---DLGPLLPSRNVS---;1;1\n-51;DLAPLLPSRNVS;---DLAPLLPSRNVS---;1;1\n-51;DGPKLPPWNVSL;----DGPKLPPWNVSL--;1;1\n-51;DGAPSLPVWNVV;---DGAPSLPVWNVV---;1;1\n-51;DGAPPLPVWNVV;---DGAPPLPVWNVV---;1;1\n-51;AYPPYLPSRFLL;---AYPPYLPSRFLL---;1;1\n-51;AVPTIPQRNYVL;----AVPTIPQRNYVL--;1;1\n-51;ARPPLPGYNKAM;----ARPPLPGYNKAM--;1;1\n-51;ARLPARNAAYLV;------ARLPARNAAYLV;1;1\n-51;APVLPFREQLLL;-----APVLPFREQLLL-;1;1\n-51;APVLPARIWYDV;-----APVLPARIWYDV-;1;1\n-51;APTLPARMYVGS;-----APTLPARMYVGS-;1;1\n-51;APRVPMRGYEVN;-----APRVPMRGYEVN-;1;1\n-51;APRLPGRSLAMV;-----APRLPGRSLAMV-;1;1\n-51;APLLPYRIGEHW;-----APLLPYRIGEHW-;1;1\n-51;APLLPIRNGTVN;-----APLLPIRNGTVN-;1;1\n-51;APKLPVRGVTSF;-----APKLPVRGVTSF-;1;1\n-51;APIVPARVMALA;-----APIVPARVMALA-;1;1\n-51;APIAPLRNGMGF;-----APIAPLRNGMGF-;1;1\n-51;APALPTRFLRDL;-----APALPTRFLRDL-;1;1\n-51;APALPMRSYVDW;-----APALPMRSYVDW-;1;1\n-51;APALPLRNDGRY;-----APALPLRNDGRY-;1;1\n-51;APAFPSRNIVLK;-----APAFPSRNIVLK-;1;1\n-51;ALVDVAPPLPVR;ALVDVAPPLPVR------;1;1\n-51;ALLVPSLPPWLW;--ALLVPSLPPWLW----;1;1\n-51;AIMPEVPQRNWV;---AIMPEVPQRNWV---;1;1\n-51;AGYAPAVPIWYM;--AGYAPAVPIWYM----;1;1\n-51;AGPRLPARADVV;----AGPRLPARADVV--;1;1\n-51;AGLPLVPLRNLL;---AGLPLVPLRNLL---;1;1\n-51;AGLPLVPLRNLI;---AGLPLVPLRNLI---;1;1\n-51;AFAGPPILPARI;-AFAGPPILPARI-----;1;1\n-51;AALPKLPFRNMT;---AALPKLPFRNMT---;1;1\n-51;AALAPATPRRAL;--AALAPATPRRAL----;1;1\n' |
| b |
| diff -r 7950e4c52972 -r 22b245c1bb94 v.1.1.0/tool_dependencies.xml --- a/v.1.1.0/tool_dependencies.xml Fri Jun 23 05:40:22 2017 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,116 +0,0 @@ -<?xml version="1.0"?> -<tool_dependency> - <package name="clustalomega" version="1.2.0"> - <install version="1.0"> - <actions_group> - <actions architecture="x86_64" os="linux"> - <action type="download_by_url">http://www.clustal.org/omega/clustalo-1.2.0-Ubuntu-x86_64</action> - <action type="shell_command">chmod 755 clustalo-1.2.0-Ubuntu-x86_64</action> - <action type="move_file"> - <source>clustalo-1.2.0-Ubuntu-x86_64</source> - <destination>$INSTALL_DIR</destination> - </action> - <action type="shell_command">sed -i "s%#clustalOmegaCommand=%clustalOmegaCommand=$INSTALL_DIR/clustalo-1.2.0-Ubuntu-x86_64%g" $REPOSITORY_INSTALL_DIR/Hammock/settings/settings.prop</action> - </actions> - <actions architecture="x86_64" os="darwin"> - <action type="download_by_url">http://www.clustal.org/omega/clustal-omega-1.2.0-macosx</action> - <action type="shell_command">chmod 755 clustalo-1.2.0-Ubuntu-x86_64</action> - <action type="move_file"> - <source>clustalo-1.2.0-Ubuntu-x86_64</source> - <destination>$INSTALL_DIR</destination> - </action> - <action type="shell_command">sed -i "s%#clustalOmegaCommand=%clustalOmegaCommand=$INSTALL_DIR/clustalo-1.2.0-Ubuntu-x86_64%g" $REPOSITORY_INSTALL_DIR/Hammock/settings/settings.prop</action> - </actions> - </actions_group> - </install> - </package> - - <package name="hmmer" version="3.1b2"> - <install version="1.0"> - <actions_group> - <actions architecture="x86_64" os="linux"> - <action type="download_by_url">http://eddylab.org/software/hmmer3/3.1b2/hmmer-3.1b2-linux-intel-x86_64.tar.gz</action> - <action type="move_file"> - <source>binaries/hmmbuild</source> - <destination>$INSTALL_DIR</destination> - </action> - <action type="move_file"> - <source>binaries/hmmsearch</source> - <destination>$INSTALL_DIR</destination> - </action> - <action type="shell_command">sed -i "s%#hmmbuildCommand=%hmmbuildCommand=$INSTALL_DIR/hmmbuild%g" $REPOSITORY_INSTALL_DIR/Hammock/settings/settings.prop</action> - <action type="shell_command">sed -i "s%#hmmsearchCommand=%hmmsearchCommand=$INSTALL_DIR/hmmsearch%g" $REPOSITORY_INSTALL_DIR/Hammock/settings/settings.prop</action> - </actions> - <actions architecture="x86_64" os="darwin"> - <action type="download_by_url">http://selab.janelia.org/software/hmmer3/3.1b1/hmmer-3.1b1-macosx-intel.tar.gz</action> - <action type="move_file"> - <source>binaries/hmmbuild</source> - <destination>$INSTALL_DIR</destination> - </action> - <action type="move_file"> - <source>binaries/hmmsearch</source> - <destination>$INSTALL_DIR</destination> - </action> - <action type="shell_command">sed -i "s%#hmmbuildCommand=%hmmbuildCommand=$INSTALL_DIR/hmmbuild%g" $REPOSITORY_INSTALL_DIR/Hammock/settings/settings.prop</action> - <action type="shell_command">sed -i "s%#hmmsearchCommand=%hmmsearchCommand=$INSTALL_DIR/hmmsearch%g" $REPOSITORY_INSTALL_DIR/Hammock/settings/settings.prop</action> - </actions> - </actions_group> - </install> - </package> - - <package name="hhsuite" version="2.0.16"> - <install version="1.0"> - <actions_group> - <actions architecture="x86_64" os="linux"> - <action type="download_by_url">http://wwwuser.gwdg.de/~compbiol/data/hhsuite/releases/all/hhsuite-2.0.16-linux-x86_64.tar.gz</action> - <action type="move_file"> - <source>bin/hhmake</source> - <destination>$INSTALL_DIR</destination> - </action> - <action type="move_file"> - <source>bin/hhsearch</source> - <destination>$INSTALL_DIR</destination> - </action> - <action type="move_file"> - <source>lib</source> - <destination>$INSTALL_DIR</destination> - </action> - <action type="shell_command">sed -i "s%#hhmakeCommand=%hhmakeCommand=$INSTALL_DIR/hhmake%g" $REPOSITORY_INSTALL_DIR/Hammock/settings/settings.prop</action> - <action type="shell_command">sed -i "s%#hhsearchCommand=%hhsearchCommand=$INSTALL_DIR/hhsearch%g" $REPOSITORY_INSTALL_DIR/Hammock/settings/settings.prop</action> - <action type="shell_command">sed -i "s%#reformatCommand=%reformatCommand=$INSTALL_DIR/lib/hh/scripts/reformat.pl%g" $REPOSITORY_INSTALL_DIR/Hammock/settings/settings.prop</action> - <action type="set_environment"> - <environment_variable name="HHLIB" action="set_to">$INSTALL_DIR/lib/hh</environment_variable> - </action> - </actions> - <actions architecture="x86_64" os="darwin"> - <action type="download_by_url">ftp://toolkit.genzentrum.lmu.de/pub/HH-suite/releases/hhsuite-2.0.16-macosx.tar.gz</action> - <action type="move_file"> - <source>bin/hhmake</source> - <destination>$INSTALL_DIR</destination> - </action> - <action type="move_file"> - <source>bin/hhsearch</source> - <destination>$INSTALL_DIR</destination> - </action> - <action type="move_file"> - <source>lib</source> - <destination>$INSTALL_DIR</destination> - </action> - <action type="shell_command">sed -i "s%#hhmakeCommand=%hhmakeCommand=$INSTALL_DIR/hhmake%g" $REPOSITORY_INSTALL_DIR/Hammock/settings/settings.prop</action> - <action type="shell_command">sed -i "s%#hhsearchCommand=%hhsearchCommand=$INSTALL_DIR/hhsearch%g" $REPOSITORY_INSTALL_DIR/Hammock/settings/settings.prop</action> - <action type="shell_command">sed -i "s%#reformatCommand=%reformatCommand=$INSTALL_DIR/lib/hh/scripts/reformat.pl%g" $REPOSITORY_INSTALL_DIR/Hammock/settings/settings.prop</action> - <action type="set_environment"> - <environment_variable name="HHLIB" action="set_to">$INSTALL_DIR/lib/hh</environment_variable> - </action> - </actions> - </actions_group> - </install> - </package> - - - - <set_environment version="1.0"> - <environment_variable name="HAMMOCK_JAR" action="set_to">$REPOSITORY_INSTALL_DIR/Hammock/dist/Hammock.jar</environment_variable> - <environment_variable name="MATRIX_PATH" action="set_to">$REPOSITORY_INSTALL_DIR/Hammock/matrices/</environment_variable> - </set_environment> -</tool_dependency> |
| b |
| diff -r 7950e4c52972 -r 22b245c1bb94 v.1.1.0/wrapper.sh --- a/v.1.1.0/wrapper.sh Fri Jun 23 05:40:22 2017 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,2 +0,0 @@ -#!/bin/sh -java -jar "$@" |
| b |
| diff -r 7950e4c52972 -r 22b245c1bb94 wrapper.sh --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/wrapper.sh Fri Jun 23 06:33:16 2017 -0400 |
| b |
| @@ -0,0 +1,2 @@ +#!/bin/sh +java -jar "$@" |