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

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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.bioperl.org/ 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/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.