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 calculated.

-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 <[email protected]>, for the Debian GNU/Linux system (but may be used by others).