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.