Dotur(1)						      General Commands Manual							  Dotur(1)

NAME

       dotur - A program for calculating descriptive statistics for sequence libraries

SYNOPSIS

       dotur [-i Iterations (<1000>)] [-c ClusterMethod (<f>, n, a)] [-p Precision (10, <100>, 1000, 10000)] [-l] [-j] <file>

OPTIONS

       -i:    Number of iterations (default = 1000)

       -c:    Clustering method - (f) furthest neighbor, (n) nearest neighbor, (a) average neighbor (default = f)

       -p:    Precision of distances for output, increasing can dramatically lengthen execution times - 10, 100, 1000, 10000 (default = 100)

       -l:    Input file is lower triangular (default = square matrix)

       -r:    Calculates rarefaction curves for each parameter, can dramatically lengthen execution times.  Simple rarefaction curve always calcu-
	      lated.

       -stop: Stops clustering when cutoff has been reached.

       -wrep: Samples with replacement.

       -jumble:
	      Jumble the order of the distance matrix.

       -sim:  Converts similarity score to distance (D=1-S).

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.

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).

DOTUR
								   June 03, 2011							  Dotur(1)