[med-svn] [phyutility] 04/05: man page edits

[Stephen Smith]

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

commit 706079b90252f743eb74ce1ca4e50d25a7966595
Author: blackrim <blackrim at gmail.com>
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

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