[med-svn] [phybin] 05/05: Add manpage

[Andreas Tille]

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tille pushed a commit to branch master
in repository phybin.

commit 2d3643a8b3a2ce40afa48ce8e86375a98aa21a67
Author: Andreas Tille <tille at debian.org>
Date:   Fri Dec 18 17:34:56 2015 +0100

    Add manpage
---
 debian/manpages |   1 +
 debian/phybin.1 | 133 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++
 2 files changed, 134 insertions(+)

diff --git a/debian/manpages b/debian/manpages
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+debian/*.1
diff --git a/debian/phybin.1 b/debian/phybin.1
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+.TH PHYBIN "1" "December 2015" "phybin 0.3" "User Commands"
+.SH NAME
+phybin \- binning/clustering newick trees by topology
+.SH SYNOPSIS
+.B phybin
+[\fI\,OPTION\/\fR...] \fI\,files or directories\/\fR...
+.SH DESCRIPTION
+PhyBin takes Newick tree files as input.  Paths of Newick files can
+be passed directly on the command line.  Or, if directories are provided,
+all files in those directories will be read.  Taxa are named based on the files
+containing them.  If a file contains multiple trees, all are read by phybin, and
+the taxa name then includes a suffix indicating the position in the file:
+.IP
+e.g. FILENAME_0, FILENAME_1, etc.
+.PP
+When clustering trees, Phybin computes a complete all\-to\-all Robinson\-Foulds distance matrix.
+If a threshold distance (tree edit distance) is given, then a flat set of clusters
+will be produced in files clusterXX_YY.tr.  Otherwise it produces a full dendogram.
+.PP
+Binning mode provides an especially quick\-and\-dirty form of clustering.
+When running with the \fB\-\-bin\fR option, only exactly equal trees are put in the same cluster.
+Tree pre\-processing still applies, however: for example collapsing short branches.
+.SS "USAGE NOTES:"
+.PP
+* Currently phybin ignores input trees with the wrong number of taxa.
+.PP
+* If given a directory as input phybin will assume all contained files are Newick trees.
+.SH OPTIONS
+.TP
+\fB\-v\fR       \fB\-\-verbose\fR
+print WARNINGS and other information (recommended at first)
+.TP
+\fB\-V\fR       \fB\-\-version\fR
+show version number
+.TP
+\fB\-o\fR DIR   \fB\-\-output\fR=\fI\,DIR\/\fR
+set directory to contain all output files (default "./phybin_out/")
+.TP
+\fB\-\-selftest\fR
+run internal unit tests
+.SS Clustering Options
+.TP
+\fB\-\-bin\fR
+Use simple binning, the cheapest form of 'clustering'
+.TP
+\fB\-\-single\fR
+Use single\-linkage clustering (nearest neighbor)
+.TP
+\fB\-\-complete\fR
+Use complete\-linkage clustering (furthest neighbor)
+.TP
+\fB\-\-UPGMA\fR
+Use Unweighted Pair Group Method (average linkage) \- DEFAULT mode
+.TP
+\fB\-\-editdist\fR=\fI\,DIST\/\fR
+Combine all clusters separated by DIST or less.  Report a flat list of clusters.
+Irrespective of whether this is activated, a hierarchical clustering (dendogram.pdf) is produced.
+.SS Select Robinson\-Foulds (symmetric difference) distance algorithm:
+.TP
+\fB\-\-hashrf\fR
+(default) use a variant of the HashRF algorithm for the distance matrix
+.TP
+\fB\-\-tolerant\fR
+use a slower, modified RF metric that tolerates missing taxa
+.SS Visualization
+.TP
+\fB\-g\fR       \fB\-\-graphbins\fR
+use graphviz to produce .dot and .pdf output files
+.TP
+\fB\-d\fR       \fB\-\-drawbins\fR
+like \fB\-g\fR, but open GUI windows to show each bin's tree
+.TP
+\fB\-w\fR       \fB\-\-view\fR
+for convenience, "view mode" simply displays input Newick files without binning
+.TP
+\fB\-\-showtrees\fR
+Print (textual) tree topology inside the nodes of the dendrogram
+.TP
+\fB\-\-highlight\fR=\fI\,FILE\/\fR
+Highlight nodes in the tree\-of\-trees (dendrogram) consistent with the.
+given tree file.  Multiple highlights are permitted and use different colors.
+.TP
+\fB\-\-interior\fR
+Show the consensus trees for interior nodes in the dendogram, rather than just points.
+.SS Tree pre\-processing
+.TP
+\fB\-\-prune\fR=\fI\,TAXA\/\fR
+Prune trees to only TAXA before doing anything else.
+Space and comma separated lists of taxa are allowed.  Use quotes.
+.TP
+\fB\-b\fR LEN   \fB\-\-minbranchlen\fR=\fI\,LEN\/\fR
+collapse branches less than LEN
+.TP
+\fB\-\-minbootstrap\fR=\fI\,INT\/\fR
+collapse branches with bootstrap values less than INT
+.SS Extracting taxa names
+.TP
+\fB\-p\fR NUM   \fB\-\-nameprefix\fR=\fI\,NUM\/\fR
+Leaf names in the input Newick trees can be gene names, not taxa.
+Then it is typical to extract taxa names from genes.  This option extracts
+a prefix of NUM characters to serve as the taxa name.
+.TP
+\fB\-s\fR STR   \fB\-\-namesep\fR=\fI\,STR\/\fR
+An alternative to \fB\-\-nameprefix\fR, STR provides a set of delimeter characters,
+for example '\-' or '0123456789'.  The taxa name is then a variable\-length
+prefix of each gene name up to but not including any character in STR.
+.TP
+\fB\-m\fR FILE  \fB\-\-namemap\fR=\fI\,FILE\/\fR
+Even once prefixes are extracted it may be necessary to use a lookup table
+to compute taxa names, e.g. if multiple genes/plasmids map onto one taxa.
+This option specifies a text file with find/replace entries of the form
+"<string> <taxaname>", which are applied AFTER \fB\-s\fR and \fB\-p\fR.
+.SS Utility Modes
+.TP
+\fB\-\-rfdist\fR
+print a Robinson Foulds distance matrix for the input trees
+.TP
+\fB\-\-setdiff\fR
+for convenience, print the set difference between cluster*.txt files
+.TP
+\fB\-\-print\fR
+simply print out a concise form of each input tree
+.TP
+\fB\-\-printnorms\fR
+simply print out a concise and NORMALIZED form of each input tree
+.TP
+\fB\-\-consensus\fR
+print a strict consensus tree for the inputs, then exit
+.TP
+\fB\-\-matching\fR
+print a list of tree names that match any \fB\-\-highlight\fR argument
+.SH AUTHOR
+This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.

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