Bio::Tools::Run::PiseApplication::dnadist
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Bioperl class for: Phylip dnadist - Compute distance matrix from nucleotide sequences (Felsenstein) References: Felsenstein, J. 1993. PHYLIP (Phylogeny Inference Package) version 3.5c. Distributed by the author. Department of Genetics, University of Washington, Seattle. Felsenstein, J. 1989. PHYLIP -- Phylogeny Inference Package (Version 3.2). Cladistics 5: 164-166. Parameters: (see also: http://bioweb.pasteur.fr/seqanal/interfaces/dnadist.html for available values): dnadist (String) infile (Sequence) Alignment File pipe: readseq_ok_alig distance (Excl) Distance (D) ratio (Integer) Transition/transversion ratio (T) gamma (Excl) Gamma distributed rates across sites (G) variation_coeff (Float) Coefficient of variation of substitution rate among sites (must be positive) (if Gamma) invariant_sites (Float) Fraction of invariant sites (if Gamma) empirical_frequencies (Switch) Use empirical base frequencies (F) base_frequencies (String) Base frequencies for A, C, G, T/U (if not empirical) (separated by commas) one_category (Switch) One category of substitution rates (C) n_categ (Integer) Number of categories (1 to 9) categ_rates (String) Rate for each category (separated by commas) weights (Switch) Use weights for sites (W) weights_file (InFile) Weights file seqboot (Switch) Perform a bootstrap before analysis method (Excl) Resampling methods seqboot_seed (Integer) Random number seed (must be odd) replicates (Integer) How many replicates matrix_form (Switch) Lower-triangular distance matrix (L) printdata (Switch) Print out the data at start of run (1) confirm (String) terminal_type (String) multiple_dataset (String) seqboot_confirm (String) seqboot_terminal_type (String)
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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.
This software is provided "as is" without warranty of any kind.
http://bioweb.pasteur.fr/seqanal/interfaces/dnadist.html
Bio::Tools::Run::PiseApplication
Bio::Tools::Run::AnalysisFactory::Pise
Bio::Tools::Run::PiseJob
Title : new() Usage : my $dnadist = Bio::Tools::Run::PiseApplication::dnadist->new($location, $email, @params); Function: Creates a Bio::Tools::Run::PiseApplication::dnadist 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 $dnadist = $factory->program('dnadist'); Example : - Returns : An instance of Bio::Tools::Run::PiseApplication::dnadist.
To install Bio::Factory::EMBOSS, copy and paste the appropriate command in to your terminal.
cpanm
cpanm Bio::Factory::EMBOSS
CPAN shell
perl -MCPAN -e shell install Bio::Factory::EMBOSS
For more information on module installation, please visit the detailed CPAN module installation guide.