- 19 Oct, 2015 1 commit
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julien veyssier authored
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- 26 Mar, 2013 1 commit
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vincent authored
correct some pb with gapOpening cost at sequence ends git-svn-id: http://162.38.181.25/svn/macse@24 65091fd0-2642-4439-a783-786ed20c9932
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- 22 Mar, 2013 2 commits
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vincent authored
git-svn-id: http://162.38.181.25/svn/macse@23 65091fd0-2642-4439-a783-786ed20c9932
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vincent authored
-add trimSequence sub programm -make enrich alignment a subfonction git-svn-id: http://162.38.181.25/svn/macse@22 65091fd0-2642-4439-a783-786ed20c9932
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- 19 Mar, 2013 2 commits
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vincent authored
git-svn-id: http://162.38.181.25/svn/macse@21 65091fd0-2642-4439-a783-786ed20c9932
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vincent authored
- begin/end gap cost all subprograms - default gc for remove gappy seq sub programs git-svn-id: http://162.38.181.25/svn/macse@20 65091fd0-2642-4439-a783-786ed20c9932
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- 23 Feb, 2013 1 commit
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vincent authored
- add guessOneReadingFrame in the NT2AA subprogram - handle profile with no sequence git-svn-id: http://162.38.181.25/svn/macse@19 65091fd0-2642-4439-a783-786ed20c9932
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- 16 Feb, 2013 1 commit
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vincent authored
- fix a minor bug in enrichAlignment (0 values was ignored as threshold) - improve translateNT2AA to allow ignoring final stop (allow standard 3 step alignment strategy) - print information concerning the genetic code used for the last sequence (last sequence information was previously missing) git-svn-id: http://162.38.181.25/svn/macse@18 65091fd0-2642-4439-a783-786ed20c9932
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- 30 Nov, 2012 1 commit
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vincent authored
git-svn-id: http://162.38.181.25/svn/macse@17 65091fd0-2642-4439-a783-786ed20c9932
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- 27 Nov, 2012 2 commits
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vincent authored
git-svn-id: http://162.38.181.25/svn/macse@16 65091fd0-2642-4439-a783-786ed20c9932
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vincent authored
git-svn-id: http://162.38.181.25/svn/macse@15 65091fd0-2642-4439-a783-786ed20c9932
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- 17 Nov, 2012 1 commit
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vincent authored
git-svn-id: http://162.38.181.25/svn/macse@14 65091fd0-2642-4439-a783-786ed20c9932
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- 31 Oct, 2012 1 commit
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vincent authored
add codingSequence basic statistic and (non parameterized) filtering during alignment enrichment based on those informations add export functionality, to replace stop codon or FS codon in NT sequences, "!" in final codon are place at its end git-svn-id: http://162.38.181.25/svn/macse@13 65091fd0-2642-4439-a783-786ed20c9932
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- 25 Oct, 2012 1 commit
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vincent authored
ProfileAligner use double instead of float to limit rounding errors git-svn-id: http://162.38.181.25/svn/macse@12 65091fd0-2642-4439-a783-786ed20c9932
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- 21 Oct, 2012 2 commits
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vincent authored
-prog enrichAlignment correct the determination of the sequence to be add git-svn-id: http://162.38.181.25/svn/macse@11 65091fd0-2642-4439-a783-786ed20c9932
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vincent authored
- prog enrichAlignment => first version, does not question sequence order (pb of memory for building huge distance matrix) git-svn-id: http://162.38.181.25/svn/macse@10 65091fd0-2642-4439-a783-786ed20c9932
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- 20 Oct, 2012 3 commits
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vincent authored
- handle the case where the subset is empty or contains all sequences - specify that a parameter follows the -out_subset and -out_other options git-svn-id: http://162.38.181.25/svn/macse@9 65091fd0-2642-4439-a783-786ed20c9932
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vincent authored
git-svn-id: http://162.38.181.25/svn/macse@8 65091fd0-2642-4439-a783-786ed20c9932
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vincent authored
- SplitAlignment allows to specify a stretch of sites (useful for isolating section during debugging), todo anonimizing seq names (pb when names contains comma) - translate NT2AA is implemented - event costs are automatically turn into negative values - minor bugs in option handling are fixed git-svn-id: http://162.38.181.25/svn/macse@7 65091fd0-2642-4439-a783-786ed20c9932
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- 19 Oct, 2012 1 commit
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vincent authored
git-svn-id: http://162.38.181.25/svn/macse@6 65091fd0-2642-4439-a783-786ed20c9932
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- 10 Oct, 2012 1 commit
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vincent authored
git-svn-id: http://162.38.181.25/svn/macse@5 65091fd0-2642-4439-a783-786ed20c9932
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- 23 Mar, 2012 1 commit
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remy authored
git-svn-id: http://162.38.181.25/svn/macse@4 65091fd0-2642-4439-a783-786ed20c9932
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- 22 Mar, 2012 1 commit
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vincent authored
git-svn-id: http://162.38.181.25/svn/macse@3 65091fd0-2642-4439-a783-786ed20c9932
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- 28 Feb, 2012 1 commit
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remy authored
git-svn-id: http://162.38.181.25/svn/macse@2 65091fd0-2642-4439-a783-786ed20c9932
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- 30 Jan, 2012 1 commit
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root authored
git-svn-id: http://162.38.181.25/svn/macse@1 65091fd0-2642-4439-a783-786ed20c9932
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