.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.16.
.TH QUICKTREE "1" "August 2020" "quicktree " "User Commands"
.SH NAME
quicktree - transforms Stockholm alignment to PHYLIP phylogenetic tree
.SH SYNOPSIS
.B quicktree
[\fI\,-options\/\fR] \fI\,<inputfile>\/\fR
.SH DESCRIPTION
A Fatal Error occurred: No such option as '\-\-help'.
.SH OPTIONS
\fB\-in\fR <m|a>        : input file is a distance matrix in phylip format (m)
.IP
or an alignment in stockholm format* (a, default)
.PP
\fB\-out\fR <m|t>       : output is a distance matrix in phylip format (m) or
.IP
a tree in New Hampshire format
.PP
Advanced options :
\fB\-upgma\fR           : Use the UPGMA method to construct the tree
.IP
(ignored for distance matrix outputs)
.PP
\fB\-kimura\fR          : Use the kimura translation for pairwise distances
.IP
(ignored for distance matrix inputs)
.PP
\fB\-boot\fR <n>        : Calcuate bootstrap values with n iterations
.IP
(ignored for distance matrix outputs)
.PP
\fB\-v\fR               : print version and exit
.PP
*Use sreformat, part of the HMMer package to convert your alignment to Stockholm format
.PP
A Fatal Error occurred: No such option as '\-\-version'.
Usage: quicktree [\-options] <inputfile>
Options:
\fB\-in\fR <m|a>        : input file is a distance matrix in phylip format (m)
.IP
or an alignment in stockholm format* (a, default)
.PP
\fB\-out\fR <m|t>       : output is a distance matrix in phylip format (m) or
.IP
a tree in New Hampshire format
.PP
Advanced options :
\fB\-upgma\fR           : Use the UPGMA method to construct the tree
.IP
(ignored for distance matrix outputs)
.PP
\fB\-kimura\fR          : Use the kimura translation for pairwise distances
.IP
(ignored for distance matrix inputs)
.PP
\fB\-boot\fR <n>        : Calcuate bootstrap values with n iterations
.IP
(ignored for distance matrix outputs)
.PP
\fB\-v\fR               : print version and exit
.PP
*Use sreformat, part of the HMMer package to convert your alignment to Stockholm format
.SH "SEE ALSO"
The full documentation for
.B quicktree
is maintained as a Texinfo manual.  If the
.B info
and
.B quicktree
programs are properly installed at your site, the command
.IP
.B info quicktree
.PP
should give you access to the complete manual.