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commit 2f7bd63bfdd25dd64227214d87f95b1b5e865904 Author: Andreas Tille <[email protected]> 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. -- 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
