Bio::Tools::Run::PiseApplication::treealign # Bio::Tools::Run::PiseApplication::treealign Bioperl class for: treealign phylogenetic alignment of homologous sequences (J. Hein) References: Hein, J.: Unified approach to alignment and phylogenies. Meth. Enzymol. 183:626-645 (1990). Hein, J.: A new method that simultaneously aligns and reconstruct ancestral sequences for any number of homologous sequences, when the phylogeny is given. Mol. Biol. Evol. 6:649-668 (1989). Hein, J.: A tree reconstruction method that is economical in the number of pairwise comparisons used. Mol. Biol. Evol. 6:669-684 (1989). Parameters: (see also: http://bioweb.pasteur.fr/seqanal/interfaces/treealign.html for available values): treealign (String) fileseq (Sequence) Sequences File pipe: seqsfile seqtype (Excl) Sequence type nuseq (Integer) Number of sequences gap_open (Integer) Gap open penalty gap_ext (Integer) Gap extension penalty ancesterout (Switch) Present ancestral sequences usertree (Switch) User tree usertreefile (InFile) Your tree file filetree (OutFile) fileali (OutFile)

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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/treealign.html Bio::Tools::Run::PiseApplication Bio::Tools::Run::AnalysisFactory::Pise Bio::Tools::Run::PiseJob

new
Title : new() Usage : my $treealign = Bio::Tools::Run::PiseApplication::treealign->new($location, $email, @params); Function: Creates a Bio::Tools::Run::PiseApplication::treealign 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 $treealign = $factory->program('treealign'); Example : - Returns : An instance of Bio::Tools::Run::PiseApplication::treealign.