.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.46.1.
.TH TREE_RECON "1" "September 2014" "tree_recon 1.4.1+dfsg" "User Commands"
.SH NAME
tree_recon \- Tree reconstruction
.PP
SYNOPSIS
.IP
tree_recon [OPTIONS] \fB\-m\fR IN.DIST
.PP
DESCRIPTION
.IP
Reconstruct phylogenetic tree from Phylip matrix IN.DIST.
.HP
\fB\-h\fR, \fB\-\-help\fR
.IP
Displays this help message.
.HP
\fB\-\-version\fR
.IP
Display version information
.IP
Input / Output:
.HP
\fB\-m\fR, \fB\-\-matrix\fR FILE
.IP
Name Phylip distance matrix file. Must contain at least three
species. Valid filetype is: dist.
.HP
\fB\-o\fR, \fB\-\-out\-file\fR FILE
.IP
Path to write output to. Valid filetypes are: dot and newick.
Default: tree.dot.
.IP
Algorithm Options:
.HP
\fB\-b\fR, \fB\-\-build\fR METHOD
.IP
Tree building method. nj: neighbour\-joining, min: UPGMA single
linkage, max: UPGMA complete linkage, avg: UPGMA average linkage,
wavg: UPGMA weighted average linkage. Neighbour\-joining creates an
unrooted tree. We root that tree at the least joined pair. One of
nj, min, max, avg, and wavg. Default: nj.
.PP
CONTACT AND REFERENCES
.IP
For questions or comments, contact:
.IP
Tobias Rausch <rausch@embl.de>
.IP
SeqAn Homepage:
.IP
http://www.seqan.de
.PP
VERSION
.IP
tree_recon version: 1.02
Last update July 17, 2012