This is an automated email from the git hooks/post-receive script. blackrim-guest pushed a commit to branch master in repository phyutility.
commit 7c1411d3b5926bad73a03f0ed77bd36fcb1374b0 Author: blackrim <[email protected]> Date: Mon Mar 24 21:30:45 2014 -0400 man page edits --- debian/phyutility.1 | 41 ++++++++++++++++++++++++----------------- 1 file changed, 24 insertions(+), 17 deletions(-) diff --git a/debian/phyutility.1 b/debian/phyutility.1 index 73608fe..d53b550 100644 --- a/debian/phyutility.1 +++ b/debian/phyutility.1 @@ -6,43 +6,50 @@ phyutility \- tools for manipulating sequences and phylogenies \fI<options>\fR \fI<command>\fR .SH DESCRIPTION You have to enter some sort of analysis -Phyutility (fyoo\-til\-i\-te) v.2.2.4 +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 trees: .IP -consensus +consensus - calculate consensus trees (use with -con -t <threshold> -in <infile> -out <outfile>) .IP -convert +convert- convert tree files (use with -vert -in <infile> -out <outfile>) .IP -leafstab +leafstab - leaf stability (use with -ls -in <infile>) +.IP linmove +lineage movement (use with -lm -names <tip names> -tree <consensus> -in <infile> -out <outfile>) .IP -linmove +prune - prune lineages (use with -pr -names <tip names> -in <infile> -out <outfile>) .IP -prune +reroot - reroot trees (use with -rr -names <tip names> -in <infile> -out <outfile>) .IP -reroot +thin - thin trees (use with -tt # -in <infile> -out <outfile>) .IP -thin -.IP -treesupp +treesupp - support for a set of trees (use with -ts -tree <tree> -in <infile> -out <outfile>) .TP seqs: .IP -clean +clean - trim seqs based on threshold (use with -clean # -in <infile> -out <outfile> -aa <to force aa>) .IP -concat +concat - concatenate alignments (use with -concat -in <infiles> -out <outfile> -aa <to force aa>) .IP -ncbiget +ncbiget - fetch seqs from NCBI (for options run phyutility -h ncbiget) .IP -ncbisearch +ncbisearch - seach NCBI (for options run phyutility -h ncbisearch) .IP -parse +parse - parse genbank results (for options run phyutility -h parse) .SH EXAMPLE -???? +.TP +java -jar phyutility.jar -con -t 0.5 -in testall.tre -out test.con +.IP +Consensus the set of trees in testall.tre collapsing branches with less than 0.5 frequency. +.TP +java -jar phyutility.jar -vert -in test.tre -out testvert.nex +.IP +Convert the tree file from newick in test.tre into nexus in testvert.nex. .SH SEE ALSO -See documentation for more information +See documentation at https://github.com/blackrim/phyutility/blob/master/manual.pdf?raw=true for more information. .SH AUTHOR Stephen A. Smith http://www.blackrim.org [email protected] -- 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
