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 ([email protected]) This manpage by Tim Booth ([email protected])

LICENCE AND COPYRIGHT

Copyright (c) 2009 ([email protected]). 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.