[med-svn] [phyutility] 02/05: man page edits

[Stephen Smith]

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

commit 77c954a49dcdea937328d83b8a483dcc295e5bc5
Author: blackrim <blackrim at gmail.com>
Date:   Mon Mar 24 21:45:11 2014 -0400

    man page edits
---
 debian/phyutility.1 | 62 +++++++++++++++++++++++++----------------------------
 1 file changed, 29 insertions(+), 33 deletions(-)

diff --git a/debian/phyutility.1 b/debian/phyutility.1
index d53b550..7da0b5c 100644
--- a/debian/phyutility.1
+++ b/debian/phyutility.1
@@ -11,43 +11,39 @@ Phyutility (fyoo\-til\-i\-te) v.2.7.3
 To get help on a specific command use option \fB\-h\fR <command>
 .SS COMMANDS
 .TP
-trees:
-.IP
-consensus - calculate consensus trees (use with -con -t <threshold> -in <infile> -out <outfile>)
-.IP
-convert- convert tree files (use with -vert -in <infile> -out <outfile>)
-.IP
-leafstab - leaf stability (use with -ls -in <infile>)
+for trees:
+.IP consensus
+Calculate consensus trees. Use like -con -t <threshold> -in <infile> -out <outfile>.
+.IP convert 
+Convert tree files. Use like -vert -in <infile> -out <outfile>.
+.IP leafstab
+Leaf stability index calculation. Use like -ls -in <infile>.
 .IP linmove
-lineage movement (use with -lm -names <tip names> -tree <consensus> -in <infile> -out <outfile>)
-.IP
-prune - prune lineages (use with -pr -names <tip names> -in <infile> -out <outfile>)
-.IP
-reroot - reroot trees (use with -rr -names <tip names> -in <infile> -out <outfile>)
-.IP
-thin - thin trees (use with -tt # -in <infile> -out <outfile>)
-.IP
-treesupp - support for a set of trees (use with -ts -tree <tree> -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>.
+.IP reroot
+Reroot trees. Use like -rr -names <tip names> -in <infile> -out <outfile>.
+.IP thin
+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>.
 .TP
-seqs:
-.IP
-clean - trim seqs based on threshold (use with -clean # -in <infile> -out <outfile> -aa <to force aa>)
-.IP
-concat - concatenate alignments (use with -concat -in <infiles> -out <outfile> -aa <to force aa>)
-.IP
-ncbiget - fetch seqs from NCBI (for options run phyutility -h ncbiget)
-.IP
-ncbisearch - seach NCBI (for options run phyutility -h ncbisearch)
-.IP
-parse - parse genbank results (for options run phyutility -h parse)
+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>.
+.IP ncbiget
+Fetch seqs from NCBI. For options run phyutility -h ncbiget.
+.IP ncbisearch
+Seach NCBI. For options run phyutility -h ncbisearch.
+.IP 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
+.IP java -jar phyutility.jar -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.
-.TP
-java -jar phyutility.jar -vert -in test.tre -out testvert.nex
-.IP
+.IP java -jar phyutility.jar -vert -in test.tre -out testvert.nex
 Convert the tree file from newick in test.tre into nexus in testvert.nex.
 .SH SEE ALSO
 See documentation at https://github.com/blackrim/phyutility/blob/master/manual.pdf?raw=true for more information.

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