Mercurial > repos > damion > ffp_phylogeny

comparison README.md @ 3:79a4a86981d3 draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author damion
date Thu, 23 Apr 2015 17:47:39 -0400
parents 671667722d3d
children
comparison
equal deleted inserted replaced
2:671667722d3d 3:79a4a86981d3
6 ------------ 6 ------------
7 7
8 FFP (Feature frequency profile) is an alignment free comparison tool for phylogenetic analysis and text comparison. It can be applied to nucleotide sequences, complete genomes, proteomes and even used for text comparison. This software is a Galaxy (http://galaxyproject.org) tool for calculating FFP on one or more fasta sequence or text datasets. 8 FFP (Feature frequency profile) is an alignment free comparison tool for phylogenetic analysis and text comparison. It can be applied to nucleotide sequences, complete genomes, proteomes and even used for text comparison. This software is a Galaxy (http://galaxyproject.org) tool for calculating FFP on one or more fasta sequence or text datasets.
9 9
10 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 . 10 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 .
11
12 **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.
11 13
12 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. 14 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.
13 15
14 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. 16 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.
15 17