.TH TREE_RECON 1 "" "tree_recon 1.4.8 [tarball]" ""
.SH NAME
tree_recon \- Tree reconstruction
.SH SYNOPSIS
\fBtree_recon\fP [\fIOPTIONS\fP] \fB-m\fP \fIIN.DIST\fP
.SH DESCRIPTION
Reconstruct phylogenetic tree from Phylip matrix \fIIN.DIST\fP.
.SH OPTIONS
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\fB-h\fP, \fB--help\fP
Display the help message.
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\fB--version\fP
Display version information.
.SS Input / Output:
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\fB-m\fP, \fB--matrix\fP \fIINPUT_FILE\fP
Name Phylip distance matrix file.  Must contain at least three species. Valid filetype is: \fI.dist\fP.
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\fB-o\fP, \fB--out-file\fP \fIOUTPUT_FILE\fP
Path to write output to. Valid filetypes are: \fI.newick\fP and \fI.dot\fP. Default: \fItree.dot\fP.
.SS Algorithm Options:
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\fB-b\fP, \fB--build\fP \fISTRING\fP
Tree building method. \fInj\fP: neighbour-joining, \fImin\fP: UPGMA single linkage, \fImax\fP: UPGMA complete linkage, \fIavg\fP: UPGMA average linkage, \fIwavg\fP: UPGMA weighted average linkage.  Neighbour-joining creates an unrooted tree.  We root that tree at the least joined pair. One of \fInj\fP, \fImin\fP, \fImax\fP, \fIavg\fP, and \fIwavg\fP. Default: \fInj\fP.
.SH CONTACT AND REFERENCES
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For questions or comments, contact:
Tobias Rausch <rausch@embl.de>
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SeqAn Homepage:
http://www.seqan.de