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commit 706079b90252f743eb74ce1ca4e50d25a7966595 Author: blackrim <[email protected]> Date: Mon Mar 24 22:03:03 2014 -0400 man page edits --- debian/phyutility.1 | 39 ++++++++++++++++++++------------------- 1 file changed, 20 insertions(+), 19 deletions(-) diff --git a/debian/phyutility.1 b/debian/phyutility.1 index 39ff225..98de4f2 100644 --- a/debian/phyutility.1 +++ b/debian/phyutility.1 @@ -10,41 +10,42 @@ Phyutility (fyoo\-til\-i\-te) v.2.7.3 .SH OPTIONS To get help on a specific command use option \fB\-h\fR <command> .SS COMMANDS -.TP -for trees: +.B for trees: .IP consensus -Calculate consensus trees. Use like -con -t <threshold> -in <infile> -out <outfile>. + Calculate consensus trees. Use like -con -t <threshold> -in <infile> -out <outfile>. .IP convert -Convert tree files. Use like -vert -in <infile> -out <outfile>. + Convert tree files. Use like -vert -in <infile> -out <outfile>. .IP leafstab -Leaf stability index calculation. Use like -ls -in <infile>. + Leaf stability index calculation. Use like -ls -in <infile>. .IP linmove -Lineage movement calculation. Use like -lm -names <tip names> -tree <consensus> -in <infile> -out <outfile>. + Lineage movement calculation. Use like -lm -names <tip names> -tree <consensus> -in <infile> -out <outfile>. .IP prune -Prune lineages. Use like -pr -names <tip names> -in <infile> -out <outfile>. + Prune lineages. Use like -pr -names <tip names> -in <infile> -out <outfile>. .IP reroot -Reroot trees. Use like -rr -names <tip names> -in <infile> -out <outfile>. + Reroot trees. Use like -rr -names <tip names> -in <infile> -out <outfile>. .IP thin -Thin trees. Use like -tt # -in <infile> -out <outfile>. + Thin trees. Use like -tt # -in <infile> -out <outfile>. .IP treesupp -Support for a set of trees. Use like -ts -tree <tree> -in <infile> -out <outfile>. + Support for a set of trees. Use like -ts -tree <tree> -in <infile> -out <outfile>. .TP -for seqs: +.B for seqs: .IP clean -Trim seqs based on threshold. Use like -clean # -in <infile> -out <outfile> -aa <to force aa>. -.IP concat -Concatenate alignments. Use like -concat -in <infiles> -out <outfile> -aa <to force aa>. + Trim seqs based on threshold. Use like -clean # -in <infile> -out <outfile> -aa <to force aa>. +.IP concat + Concatenate alignments. Use like -concat -in <infiles> -out <outfile> -aa <to force aa>. .IP ncbiget -Fetch seqs from NCBI. For options run phyutility -h ncbiget. + Fetch seqs from NCBI. For options run phyutility -h ncbiget. .IP ncbisearch -Seach NCBI. For options run phyutility -h ncbisearch. + Seach NCBI. For options run phyutility -h ncbisearch. .IP parse -Parse genbank results. For options run phyutility -h parse. + Parse genbank results. For options run phyutility -h parse. .SH EXAMPLE -.IP "java -jar phyutility.jar -con -t 0.5 -in testall.tre -out test.con" +.IP "phyutility -con -t 0.5 -in testall.tre -out test.con" Consensus the set of trees in testall.tre collapsing branches with less than 0.5 frequency. -.IP "java -jar phyutility.jar -vert -in test.tre -out testvert.nex" +.IP "phyutility -vert -in test.tre -out testvert.nex" Convert the tree file from newick in test.tre into nexus in testvert.nex. +.IP "phyutility -concat -in test.aln test2.aln -out testall.nex" +Concatenate 2 alignment files into nexus in testall.nex. .SH SEE ALSO See documentation at https://github.com/blackrim/phyutility/blob/master/manual.pdf?raw=true for more information. .SH AUTHOR -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/phyutility.git _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
