Mercurial > repos > damion > ffp_phylogeny
diff README.md @ 3:79a4a86981d3 draft default tip
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| author | damion |
|---|---|
| date | Thu, 23 Apr 2015 17:47:39 -0400 |
| parents | 671667722d3d |
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--- a/README.md Fri Mar 20 14:27:19 2015 -0400 +++ b/README.md Thu Apr 23 17:47:39 2015 -0400 @@ -9,6 +9,8 @@ The original command line ffp-phylogeny code is at http://ffp-phylogeny.sourceforge.net/ . This tool uses Aaron Petkau's modified version: https://github.com/apetkau/ffp-3.19-custom . Aaron has quite a good writeup of the technique as well at https://github.com/apetkau/microbial-informatics-2014/tree/master/labs/ffp-phylogeny . +**Installation Note** : Your Galaxy server will need the groff package to be installed on it first (to generate ffp-phylogeny man pages). A cryptic error will occur if it isn't: "troff: fatal error: can't find macro file s". This is different from the "groff-base" package. + This Galaxy tool prepares a mini-pipeline consisting of **[ffpry | ffpaa | ffptxt] > [ ffpfilt | ffpcol > ffprwn] > ffpjsd > ffptree** . The last step is optional - by deselecting the "Generate Tree Phylogeny" checkbox, the tool will output a distance matrix rather than a Newick (.nhx) formatted tree file. Each sequence or text file has a profile containing tallies of each feature found. A feature is a string of valid characters of given length.