[med-svn] [phyutility] 01/05: man page edits

[Stephen Smith]

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blackrim-guest pushed a commit to branch master
in repository phyutility.

commit 7c1411d3b5926bad73a03f0ed77bd36fcb1374b0
Author: blackrim <blackrim at gmail.com>
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 eebsmith at umich.edu

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