'\" t
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.\" Copyright (C), 2011, Thorsten Alteholz <debian@alteholz.de>
.\"
.\" You may distribute under the terms of the GNU General Public
.\" License as specified in the file COPYING that comes with the
.\" man_db distribution.
.\"
.\"
.TH Dotur 1 "June 03, 2011" "DOTUR"
.SH NAME
.B dotur
\- A program for calculating descriptive statistics for sequence libraries

.SH SYNOPSIS
.B dotur
[\fI-i Iterations (<1000>)\fR] [\fI-c ClusterMethod (<f>, n, a)\fR] [\fI-p Precision (10, <100>, 1000, 10000)\fR] [\fI-l\fR] [\fI-j\fR] \fI<file>\fR
.SH OPTIONS
.TP
\fB\-i\fR:
Number of iterations (default = 1000)
.TP
\fB\-c\fR:
Clustering method \- (f) furthest neighbor, (n) nearest neighbor,
(a) average neighbor (default = f)
.TP
\fB\-p\fR:
Precision of distances for output, increasing can dramatically
lengthen execution times \- 10, 100, 1000, 10000 (default = 100)
.TP
\fB\-l\fR:
Input file is lower triangular (default = square matrix)
.TP
\fB\-r\fR:
Calculates rarefaction curves for each parameter, can dramatically
lengthen execution times.  Simple rarefaction curve always calculated.
.HP
\fB\-stop\fR: Stops clustering when cutoff has been reached.
.HP
\fB\-wrep\fR: Samples with replacement.
.TP
\fB\-jumble\fR:
Jumble the order of the distance matrix.
.TP
\fB\-sim\fR:
Converts similarity score to distance (D=1\-S).

.SH DESCRIPTION
This is the Debian GNU/Linux version of dotur.

DOTUR is a computer program that takes a distance matrix describing
the genetic distance between DNA sequence data and assigns sequences to
operational taxonomic units (OTUs) using either the furthest, average,
or nearest neighbor algorithms for all possible distances that can be
described using the distance matrix.  Using the OTU composition data,
DOTUR constructs collector's and rarefaction curves for sampling
intensity, richness estimators, and diversity indices.

.SH AUTHOR
This manual page was compiled from the package description
and the output of help2man by Thorsten Alteholz <debian@alteholz.de>,
for the Debian GNU/Linux system (but may be used by others).