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commit 77c954a49dcdea937328d83b8a483dcc295e5bc5 Author: blackrim <[email protected]> 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. -- 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
