Bio::Tools::Run::PiseApplication::fastdnaml.3pm

Langue: en

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Version: 2008-11-10 (debian - 07/07/09)

Section: 3 (Bibliothèques de fonctions)

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NAME

Bio::Tools::Run::PiseApplication::fastdnaml

SYNOPSIS

   #

DESCRIPTION

Bio::Tools::Run::PiseApplication::fastdnaml 
       Bioperl class for:
 
         fastDNAml       construction of phylogenetic trees of DNA sequences using maximum likelihood (Olsen, Matsuda, Hagstrom, Overbeek)
 
         References:
 
                 Olsen, G. J., Matsuda, H., Hagstrom, R., and Overbeek, R.  1994.  fastDNAml: A tool for construction of phylogenetic trees of DNA sequences using maximum likelihood.  Comput. Appl. Biosci. 10: 41-48.
 
                 Felsenstein, J.  1981.  Evolutionary trees from DNA sequences:   A maximum likelihood approach.  J. Mol. Evol. 17: 368-376.
 
 
 
       Parameters: 
 
         (see also:
           http://bioweb.pasteur.fr/seqanal/interfaces/fastdnaml.html 
          for available values):
 
 
                 fastdnaml (String)
 
                 clean_tmp (String)
 
                 alignment (Sequence)
                         Sequence Alignment File
                         pipe: readseq_ok_alig
 
                 frequencies (Switch)
                         Instructs the program to use empirical base frequencies derived from the sequence data
 
                 fA (Float)
                         frequency of A (instead of empirical frequencies)
 
                 fC (Float)
                         frequency of C (instead of empirical frequencies)
 
                 fG (Float)
                         frequency of G (instead of empirical frequencies)
 
                 fT (Float)
                         frequency of T (instead of empirical frequencies)
 
                 outgroup (Integer)
                         Use the specified sequence number for the outgroup
 
                 transition (Integer)
                         ratio of transition to transversion type substitutions
 
                 jumble (Switch)
                         Randomize the sequence addition order (jumble)
 
                 non_interleaved (Switch)
                         Interleaved format
 
                 bootstrap (Switch)
                         generates a re-sample of the input data (bootstrap)
 
                 nboots (Integer)
                         how many samples
 
                 bootstrap_seed (Integer)
                         random number seed for bootstrap
 
                 nbest (Integer)
                         nbest: input order is jumbled (up to maxjumble times) until same tree is found n_best times
 
                 maxjumble (Integer)
                         maximum attempts at replicating inferred tree (max jumble)
 
                 concat (String)
 
                 in_file (String)
 
                 outfile (OutFile)
                         Output File
 
                 treefile (Switch)
                         Save tree in treefile
 
                 printdata (Switch)
                         Echo of the data in addition to the usual output (printdata)
 
                 quickadd (Switch)
                         Decreases the time in initially placing a new sequence in the growing tree (quickadd)
 
                 global (Switch)
                         global rearrangements
 
                 final_arrgt (Integer)
                         number of branches to cross in rearrangements of the completed tree
 
                 partial_arrgt (Integer)
                         number of branches to cross in testing rearrangements during the sequential addition phase of tree inference
 
                 categories (InFile)
                         categories file
 
                 weights (InFile)
                         weights file (user-specified column weighting information)
 
                 weights_categories (InFile)
                         Adds both the userweights and categories from a file
 
                 user_tree (InFile)
                         User tree - tree(s) file
 
                 user_lengths (Switch)
                         user trees to be read with branch lengths

FEEDBACK

Mailing Lists

User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated. 
   bioperl-l@bioperl.org                  - General discussion
   http://bioperl.org/wiki/Mailing_lists  - About the mailing lists

Reporting Bugs

Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web: 
   http://bugzilla.open-bio.org/

AUTHOR

Catherine Letondal (letondal@pasteur.fr) Copyright (C) 2003 Institut Pasteur & Catherine Letondal. All Rights Reserved.

This module is free software; you can redistribute it and/or modify it under the same terms as Perl itself.

DISCLAIMER

This software is provided ``as is'' without warranty of any kind.

SEE ALSO

•
http://bioweb.pasteur.fr/seqanal/interfaces/fastdnaml.html
•
Bio::Tools::Run::PiseApplication
•
Bio::Tools::Run::AnalysisFactory::Pise
•
Bio::Tools::Run::PiseJob

new

  Title   : new()
  Usage   : my $fastdnaml = Bio::Tools::Run::PiseApplication::fastdnaml->new($location, $email, @params);
  Function: Creates a Bio::Tools::Run::PiseApplication::fastdnaml object.
            This method should not be used directly, but rather by 
            a Bio::Tools::Run::AnalysisFactory::Pise instance.
            my $factory = Bio::Tools::Run::AnalysisFactory::Pise->new();
            my $fastdnaml = $factory->program('fastdnaml');
  Example : -
  Returns : An instance of Bio::Tools::Run::PiseApplication::fastdnaml.