AMPLICONNOISE(1)					    AmpliconNoise Documentation 					  AMPLICONNOISE(1)

NAME

       AmpliconNoise - remove noise from high throughput nucleotide sequence data

VERSION

       This documentation refers to version 1.22

SYNOPSIS

       See /usr/share/doc/ampliconnoise/Doc.pdf.gz for details of how to run.

DESCRIPTION

       The following tools are included.  Most of them have an MPI equivalent, for example SeqNoise has an equivalent SeqNoiseM which can be used
       with mpirun.

       FastaUnique - dereplicates fasta file
	 -in	 string 	   input file name
	Options:

       FCluster
	 -in	string		  distance input file name
	 -out	string		  output file stub
	Options:
	 -r			  resolution
	 -a			  average linkage
	 -w			  use weights
	 -i			  read identifiers
	 -s			  scale dist.

       NDist - pairwise Needleman-Wunsch sequence distance matrix from a fasta file
	 -in	 string 	   fata file name
	Options:
	 -i output identifiers

       Perseus - slays monsters
	 -sin	  string	    seq file name
	Options:
	 -tin	  string	    reference sequence file
	 -a			    output alignments
	 -d			    use imbalance
	 -rin	  string	    lookup file name

       PyroDist - pairwise distance matrix from flowgrams
	 -in	 string 	   flow file name
	 -out	 stub		   out file stub
	Options:
	 -ni			   no index in dat file
	 -rin	 string 	   lookup file name

       PyroNoise - clusters flowgrams without alignments
	 -din	  string	    flow file name
	 -out	  string	    cluster input file name
	 -lin	  string	    list file
	Options:
	 -v	  verbose
	 -c	  double	    initial cut-off
	 -ni			    no index in dat file
	 -s	  double	    precision
	 -rin	  file		    lookup file name

       SeqDist - pairwise distance matrix from a fasta file
	 -in	 string 	   fasta file name
	Options:
	 -i output identifiers
	 -rin	 string 	   lookup file name

       SeqNoise - clusters sequences
	 -in	  string	    sequence file name
	 -din	  string	    distance matrix file name
	 -out	  string	    cluster input file name
	 -lin	  string	    list file
	Options:
	 -min	    mapping file
	 -v	  verbose
	 -c	  double	    initial cut-off
	 -s	  double	    precision
	 -rin	  string	    lookup file name

       SplitClusterEven
	 -din	 string  dat filename
	 -min	 string  map filename
	 -tin	 string  tree filename
	 -s	 split size
	 -m	 min   size

AUTHOR

       All software by Chris Quince (quince@civil.gla.ac.uk) This manpage by Tim Booth	(tbooth@ceh.ac.uk)

LICENCE AND COPYRIGHT

       Copyright (c) 2009  (quince@civil.gla.ac.uk). All rights reserved.

       Released under the Lesser GPL.

       Permission is granted for anyone to copy, use, or modify these programs and documents for purposes of research or education, provided this
       copyright notice is retained, and note is made of any changes that have been made.

perl v5.12.4							    2011-04-28							  AMPLICONNOISE(1)