# HG changeset patch
# User dcorreia
# Date 1458036470 14400
# Node ID ab2cf9c6c4f1bc7c6c005e6d468584ff5075b44d
Imported from capsule None
diff -r 000000000000 -r ab2cf9c6c4f1 noisy.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/noisy.xml Tue Mar 15 06:07:50 2016 -0400
@@ -0,0 +1,167 @@
+
+ Cleaning aligned sequences
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+ noisy
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+0.80<)
+ --distance STRING Distance methode used by NeighbotNet.
+ (default is >HAMMING< [HAMMING|GTR])
+ -h, --help Print usage message for noisy.
+ --matrix FILE Use distance matrix for NeighbotNet from FILE.
+ (default is >calculate distances with nnet<)
+ --missing STRING Set list of missing characters to STRING.
+ (default is >N<)
+ --nogap Don't count gap symbol as character state.
+ (default is >0<)
+ --noconstant Ignore constant columns in output alignment.
+ (default is >0<)
+ --ordering STRING
+ Choose ordering method.
+ (default is >nnet<)
+ nnet NeighborNet
+ qnet QNet algorithm is O(n^4) both in time and memory, be careful when you use this option.
+ rand[,INT] sample INT random permutation. With rand a random sample of all possible orderings of the TAXA can be specified for which the reliability score is calculated
+ (default is >1000<)
+ INT,INT,... provide ordering explicitly as comma-seperated list of TAXA indices in the range (e.g 3,0,4,1,2 as ordering for the 5 TAXA in the input MSA).
+ all all permutations, If all is used than for all possible permutations of the TAXA the reliability score is calculated (Note that for more than 8 TAXA this can become rather time consuming!).
+
+ --shuffles INT Perform INT random shuffles per column.
+ (default is >0<)
+ -s, --silent Turn off status bar
+ (default is >0<)
+ --smooth INT Running avarage over INT columns.
+ (default is >1<)
+ --seqtype CHAR Set sequence type of input alignment to CHAR
+ (default is >D<) [D=DNA, P=Protein, R=RNA]
+ -v, --verbose Verbose mode. Causes noisy to print debugging
+ messages about its progress.
+]]>
+
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+ 10.1186/1748-7188-3-7
+ 10.1093/molbev/msl180
+ 10.1093/molbev/msh018s
+
+
diff -r 000000000000 -r ab2cf9c6c4f1 test-data/aln.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/aln.fasta Tue Mar 15 06:07:50 2016 -0400
@@ -0,0 +1,35 @@
+>TestSequence1
+ERNECFLKHKDDDPNLPPVVKPEPEALCTAFQENNNKFLENYLYEVARRHPYFYGPELLY
+YVKQ--YKAILTECCQAACCQAADKATCLAPKAKVLKEKLLASSAKQRHKCASIQKFGER
+AFKAWSIARLSQRFPKADFMDLSKLVTDLSKIHKECCHGDLLECADDREDLAKYV---QD
+SFSSKLKECCDKPLLEKSHCISELENDDLPNDLPSITTDFVEDKDVCKLLNYKEAKDVFL
+GTFLYEYSRRHPEYAVSLLLRIAKGYEATLERCCATDDAHACYSKVFDELQPLVDEPQ--
+KLMKRNCELFENLGAYGFQNALIIRYTKKMPQVSTPTLLVISKELANMGNKCCTLPESKR
+>TestSequence2
+ERADCFASHRDDNPGFPLMVRPPVDELCASYQADAQMFAGKYLYEVARRYPYFYAPELLY
+YAQKLLYKDALAEC-----CSAADKAACLTPKIDDLKESVMTSGAKQRFKCAGIEKFGER
+AFKAWAVARLSQKFPNADFAEISKIVTDLTKINKECCHGDLLECADDRVELGKYMCDNKD
+SISSKLGKCCEKPLLEKGHCIAELERDDMPADLSPIEADFVEDKEVCK--NYAEAKDVFL
+GTFLYELSRRHPEYSVVMLLRLAKGYEAVLEKCCATGDPPACYAKVFDELKPLIDEPQ--
+NLVKHNCELYGNLQEYGFQNALLIRYTKKMPQ---PTLVEVSRNLGKVGTKCCSLAEGER
+>TestSequence3
+ERNECFLSHKDDSPDLPKL-KPDPNTLCDEFKADEKKFWGKYLYEIARRHPYFYAPELLY
+YANK--YNGVFQEC-----CQAEDKGACLLPKIETMREKVLTSSARQRLRCASIQKFGER
+ALKAWSVARLSQKFPKAEFVEVTKLVTDLTKVHKECCHGDLLECADDRADLAKYICDNQD
+TISSKLKECCDKPLLEKSHCIAEVEKDAVPENLPPLTADFAEDKDVCK--NYQEAKDAFL
+GSFLYEYSRRHPE-YVLLRLALLKEYEATLEECCAKDDPHACYSTVFDKLKHLVDEPQ--
+NLIKQNCDQFEKLGEYGFQNALIVRYTRKVPQVSTPTLVEVSRSLGKVGTRCCTKPESER
+>TestSequence4
+ERNECFLQHKDDNPNLPRLVRPEVDVMCTAFHDNEETFLKKYLYEIARRHPYFYAPELLF
+FAKR--YKAAFTEC-----CQAADKAACLLPKLDELRDEGKASSAKQRLKCASLQKFGER
+AFKAWAVARLSQRFPKAEFAEVSKLVTDLTKVHTECCHGDLLECADDRADLAKYICENQD
+SISSKLKECCEKPLLEKSHCIAEVENDEMPADLPSLAADFVESKDVCK--NYAEAKDVFL
+GMFLYEYARRHPRESVVLLLRLAKTYETTLEKCCAAADPHECYAKVFDEFKPLVEEPQLL
+NLIKQNCELFEQLGEYKFQNALLVRYTKKVPQVSTPTLVEVSRNLGKVGSKCCKHPEAKR
+>TestSequence5
+ERNECFLQHKDDNPGFGQLVTPEADAMCTAFHENEQRFLGKYLYEIARRHPYFYAPELLY
+YAEE--YKGVFTEC-----CEAADKAACLTPKVDALREKVLASSAKERLKCASLQKFGER
+AFKAWSVARLSQKFPKAEFAEISKLVTDLAKIHKECCHGDLLECADDRADLAKYICENQD
+SISTKLKECCGKPVLEKSHCISEVERDELPADLPPLAVDFVEDKEVCK--NYQEAKDVFL
+GTFLYEYSRRHPS-SVSLLLRLAKEYEATLEKCCATDDPPACYAHVFDEFKPLVEEPH--
+NLVKTNCELFEKLGEYGFQNALLVRYTKKVPQVSTPTLVEVSRSLGKVGSKCCTHPEAER
\ No newline at end of file
diff -r 000000000000 -r ab2cf9c6c4f1 test-data/aln_out.fas
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/aln_out.fas Tue Mar 15 06:07:50 2016 -0400
@@ -0,0 +1,10 @@
+>TestSequence1
+ERNCFHDDPPCNFNYLYEARRPYFYPELLYKECCADKCLPKSARCAKFGERAKAWARLSQFPKAFKVTDLKHECCHGDLLECADDRLKY-DSKLCCKPLEKHCIEEDPDLDFEKVCKYEAKDFLGFLYERRHPVLKYELECCADCYVFDLEPKLKCLYFQALRYTKPQPTLSLNGCCER
+>TestSequence5
+ERNCFHDDPPCNFKYLYEARRPYFYPELLYKECCADKCLPKSARCAKFGERAKAWARLSQFPKAFKVTDLKHECCHGDLLECADDRLKYNDSKLCCKPLEKHCIEEDPDLDFEKVCKYEAKDFLGFLYERRHPVLKYELECCADCYVFDLEPNLKCLYFQALRYTKPQPTLSLKGCCER
+>TestSequence2
+ERACFHDDPPCDFKYLYEARRPYFYPELLYKECCADKCLPKSARCAKFGERAKAWARLSQFPNAFKVTDLKNECCHGDLLECADDRLKYNDSKLCCKPLEKHCIEEDPDLDFEKVCKYEAKDFLGFLYERRHPVLKYELECCADCYVFDLEPNLKCLYFQALRYTKPQPTLSLKGCCER
+>TestSequence3
+ERNCFHDDPPCDFKYLYEARRPYFYPELLYNECCADKCLPKSARCAKFGERAKAWARLSQFPKAFKVTDLKHECCHGDLLECADDRLKYNDSKLCCKPLEKHCIEEDPNLDFEKVCKYEAKDFLGFLYERRHPVLKYELECCADCYVFDLEPNLKCLYFQALRYTKPQPTLSLKGCCER
+>TestSequence4
+ERNCFHDDPPCNFKYLYEARRPYFYPELLYKECCADKCLPKSARCAKFGERAKAWARLSQFPKAFKVTDLKHECCHGDLLECADDRLKYNDSKLCCKPLEKHCIEEDPDLDFEKVCKYEAKDFLGFLYERRHPVLKYELECCADCYVFDLEPNLKCLYFQALRYTKPQPTLSLKGCCER
diff -r 000000000000 -r ab2cf9c6c4f1 tool_dependencies.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml Tue Mar 15 06:07:50 2016 -0400
@@ -0,0 +1,6 @@
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