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

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.