[med-svn] [phyutility] 01/02: Man distinguishes between hyphen and minus sign

[Andreas Tille]

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tille pushed a commit to branch master
in repository phyutility.

commit 2f7bd63bfdd25dd64227214d87f95b1b5e865904
Author: Andreas Tille <tille at debian.org>
Date:   Tue Mar 25 08:55:14 2014 +0100

    Man distinguishes between hyphen and minus sign
---
 debian/phyutility.1 | 32 ++++++++++++++++----------------
 1 file changed, 16 insertions(+), 16 deletions(-)

diff --git a/debian/phyutility.1 b/debian/phyutility.1
index e6fd34d..3e07852 100644
--- a/debian/phyutility.1
+++ b/debian/phyutility.1
@@ -11,39 +11,39 @@ To get help on a specific command use option \fB\-h\fR <command>
 .SS COMMANDS
 .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
 .B for seqs:
 .IP clean
- Trim seqs based on threshold. Use like -clean # -in <infile> -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>.
+ 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 "phyutility -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 "phyutility -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"
+.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.

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