| Next changeset 1:d90f4809ccc6 (2015-08-28) |
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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/settings-hhalign.txt 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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| diff -r 000000000000 -r b1ac138f0287 Hammock/dist/Hammock.jar |
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| Binary file Hammock/dist/Hammock.jar has changed |
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| diff -r 000000000000 -r b1ac138f0287 Hammock/matrices/blosum100.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/Hammock/matrices/blosum100.txt Mon Jan 26 06:24:21 2015 -0500 |
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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 000000000000 -r b1ac138f0287 Hammock/matrices/blosum30.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/Hammock/matrices/blosum30.txt Mon Jan 26 06:24:21 2015 -0500 |
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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 000000000000 -r b1ac138f0287 Hammock/matrices/blosum35.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/Hammock/matrices/blosum35.txt Mon Jan 26 06:24:21 2015 -0500 |
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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 000000000000 -r b1ac138f0287 Hammock/matrices/blosum40.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/Hammock/matrices/blosum40.txt Mon Jan 26 06:24:21 2015 -0500 |
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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 000000000000 -r b1ac138f0287 Hammock/matrices/blosum45.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/Hammock/matrices/blosum45.txt Mon Jan 26 06:24:21 2015 -0500 |
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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 000000000000 -r b1ac138f0287 Hammock/matrices/blosum50.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/Hammock/matrices/blosum50.txt Mon Jan 26 06:24:21 2015 -0500 |
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| @@ -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 |
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| diff -r 000000000000 -r b1ac138f0287 Hammock/matrices/blosum55.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/Hammock/matrices/blosum55.txt Mon Jan 26 06:24:21 2015 -0500 |
| 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 000000000000 -r b1ac138f0287 Hammock/matrices/blosum60.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/Hammock/matrices/blosum60.txt Mon Jan 26 06:24:21 2015 -0500 |
| 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 000000000000 -r b1ac138f0287 Hammock/matrices/blosum62.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/Hammock/matrices/blosum62.txt Mon Jan 26 06:24:21 2015 -0500 |
| 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 000000000000 -r b1ac138f0287 Hammock/matrices/blosum62.txt~ --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/Hammock/matrices/blosum62.txt~ Mon Jan 26 06:24:21 2015 -0500 |
| 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 000000000000 -r b1ac138f0287 Hammock/matrices/blosum65.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/Hammock/matrices/blosum65.txt Mon Jan 26 06:24:21 2015 -0500 |
| 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 000000000000 -r b1ac138f0287 Hammock/matrices/blosum70.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/Hammock/matrices/blosum70.txt Mon Jan 26 06:24:21 2015 -0500 |
| 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 000000000000 -r b1ac138f0287 Hammock/matrices/blosum75.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/Hammock/matrices/blosum75.txt Mon Jan 26 06:24:21 2015 -0500 |
| 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 000000000000 -r b1ac138f0287 Hammock/matrices/blosum80.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/Hammock/matrices/blosum80.txt Mon Jan 26 06:24:21 2015 -0500 |
| 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 000000000000 -r b1ac138f0287 Hammock/matrices/blosum85.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/Hammock/matrices/blosum85.txt Mon Jan 26 06:24:21 2015 -0500 |
| 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 000000000000 -r b1ac138f0287 Hammock/matrices/blosum90.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/Hammock/matrices/blosum90.txt Mon Jan 26 06:24:21 2015 -0500 |
| 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 000000000000 -r b1ac138f0287 Hammock/matrices/gonnet250.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/Hammock/matrices/gonnet250.txt Mon Jan 26 06:24:21 2015 -0500 |
| 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 000000000000 -r b1ac138f0287 Hammock/matrices/mcla71.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/Hammock/matrices/mcla71.txt Mon Jan 26 06:24:21 2015 -0500 |
| 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 000000000000 -r b1ac138f0287 Hammock/matrices/pam250.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/Hammock/matrices/pam250.txt Mon Jan 26 06:24:21 2015 -0500 |
| [ |
| @@ -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 000000000000 -r b1ac138f0287 Hammock/settings/settings-hhalign.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/Hammock/settings/settings-hhalign.txt Mon Jan 26 06:24:21 2015 -0500 |
| b |
| @@ -0,0 +1,1 @@ +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 500000 -local -mact 0.0 -p 0 |
| b |
| diff -r 000000000000 -r b1ac138f0287 Hammock/settings/settings.prop --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/Hammock/settings/settings.prop Mon Jan 26 06:24:21 2015 -0500 |
| [ |
| @@ -0,0 +1,26 @@ +#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= +#hhalignOutDirectory= +#hhsearchOutDirectory= +#fastaDatabaseFile= +#Tool parameters. Generally, it is not recommended to change this section. +clustalOmegaParameters= +hmmbuildParameters=--enone --fragthresh 1.0 --hand --wnone --amino +hmmsearchParameters=--nobias --F1 0.5 --F2 0.05 --F3 1e-2 --nonull2 +hmmalignParameters=--outformat selex --amino +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 -BLOSUM65 |
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| diff -r 000000000000 -r b1ac138f0287 Hammock/settings/settings.prop~ --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/Hammock/settings/settings.prop~ Mon Jan 26 06:24:21 2015 -0500 |
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| @@ -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 |
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| diff -r 000000000000 -r b1ac138f0287 hammock.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/hammock.xml Mon Jan 26 06:24:21 2015 -0500 |
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| b'@@ -0,0 +1,323 @@\n+<tool id="hammock_1.0" name="Hammock - cluster peptides">\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\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_greedy_params.set_greedy_params == "set":\n+\t\t-x $advanced_greedy_params.max_shift\n+\t\t-p $advanced_greedy_params.shift_penalty\n+\t\t-m \\${MATRIX_PATH}${advanced_greedy_params.scoring_matrix}.txt\n+ \t#if $advanced_greedy_params.greedy_params.set_greedy == "set":\n+ \t-g $advanced_greedy_params.greedy_params.greedy_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+\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#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 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 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+ <when value="set">\n+ \t\t<repeat name="round_labels" title="Label">\n+\t\t\t\t\t\t<param name="label" type="text" value="" label="Sequence label"/>\n+\t\t\t\t\t</repeat>\n+\t\t\t</when>\n+</conditional>\n+\n+\n+<conditional name="advanced_greedy_params">\n+ <param name="set_greedy_params" type="select" label="Greedy clustering options">\n+ <option value="auto">Default - automatic settings</option>\n+ <option value="set">Set manually</option>\n+ </param>\n+ <when value="auto" />\n+\t <w'..b'ue="true" />\n+ \t\t<when value="false" />\n+\t\t</conditional>\n+\t</when>\n+</conditional>\n+\n+</inputs>\n+\n+ <outputs> \n+ <data format="csv" name="output_clusters" />\n+\t<data format="csv" name="output_sequences" />\n+ </outputs>\n+\n+ <requirements>\n+ <requirement type="set_environment">HHLIB</requirement>\n+\t\t<requirement type="set_environment">HAMMOCK_JAR</requirement>\n+\t\t<requirement type="set_environment">MATRIX_PATH</requirement>\n+\t\t<requirement type="package" version="1.6.0">java</requirement>\n+\t\t<requirement type="package" version="1.2.0">clustalomega</requirement>\n+\t\t<requirement type="package" version="3.1b1">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_greedy_params.max_shift" value="3" />\n+\t\t<param name="advanced_greedy_params.shift_penalty" value="0" />\n+\t\t<param name="advanced_greedy_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 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 A, et al. *in preparation* \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 two files, both are semicolon-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 sequence plus header. 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+\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' |
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| diff -r 000000000000 -r b1ac138f0287 test-data/input.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/input.fa Mon Jan 26 06:24:21 2015 -0500 |
| 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 000000000000 -r b1ac138f0287 test-data/output_clusters.csv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/output_clusters.csv Mon Jan 26 06:24:21 2015 -0500 |
| b |
| @@ -0,0 +1,3 @@ +cluster_id;main_sequence;sum;no_label +43;AAMFLRPLPAVQ;1738;1738 +51;AALAPATPRRAL;415;415 |
| b |
| diff -r 000000000000 -r b1ac138f0287 test-data/output_sequences.csv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/output_sequences.csv Mon Jan 26 06:24:21 2015 -0500 |
| 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 000000000000 -r b1ac138f0287 tool_dependencies.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_dependencies.xml Mon Jan 26 06:24:21 2015 -0500 |
| 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" $REPOSITORY_INSTALL_DIR/Hammock/settings/settings.prop</action> + </actions> + </actions_group> + </install> + </package> + + <package name="hmmer" version="3.1b1"> + <install version="1.0"> + <actions_group> + <actions architecture="x86_64" os="linux"> + <action type="download_by_url">http://selab.janelia.org/software/hmmer3/3.1b1/hmmer-3.1b1-linux-intel-x86_64.tar.gz</action> + <action type="move_file"> + <source>binaries/hmmbuild</source> + <destination>$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" $REPOSITORY_INSTALL_DIR/Hammock/settings/settings.prop</action> + </actions> + </actions_group> + </install> + </package> + + <package name="hhsuite" version="2.0.16"> + <install version="1.0"> + <actions_group> + <actions architecture="x86_64" os="linux"> + <action type="download_by_url">ftp://toolkit.genzentrum.lmu.de/pub/HH-suite/releases/hhsuite-2.0.16-linux-x86_64.tar.gz</action> + <action type="move_file"> + <source>bin/hhmake</source> + <destination>$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 000000000000 -r b1ac138f0287 wrapper.sh --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/wrapper.sh Mon Jan 26 06:24:21 2015 -0500 |
| b |
| @@ -0,0 +1,2 @@ +#!/bin/sh +java -jar "$@" |