Bio::Tools::Run::PiseApplication::tipdate # Bio::Tools::Run::PiseApplication::tipdate Bioperl class for: TipDate Analysis of trees with dated tips (Andrew Rambaut) References: Andrew Rambaut, 2000. Estimating the rate of molecular evolution: Incorporating non-contemporaneous sequences into maximum likelihood phylogenies. Bioinformatics. Parameters: (see also: http://bioweb.pasteur.fr/seqanal/interfaces/tipdate.html for available values): tipdate (String) alignment (Sequence) Alignment file pipe: readseq_ok_alig model (Excl) MODEL (-m) constant_rate (Switch) Molecular clock model (SR model) (-k) change_rate (Excl) Estimate rate of change of rate (VRDT model: requires dated tips) change_rate_value (Integer) You may provide a constant rate value (-w #) absolute_rate (Float) Estimate absolute rate of substitution (SRDT model: requires dated tips) (+s)Absolute rate of molecular evolution (requires dated tips) (-s) absolute_rate_value (Integer) specify absolute rate of substitution (-s #) likelihood_root (Switch) Estimate maximum likelihood root (requires molecular clock) absolute_root_value (Integer) root with specified outgroup taxa (requires molecular clock) (-r #) absolute_rate (Float) Estimate absolute rate of substitution (SRDT model: requires dated tips) (+s)Absolute rate of molecular evolution (requires dated tips) (-s) estimate_root (Switch) Estimate maximum likelihood root (requires molecular clock) (+r) outgroup (Integer) Root with specified outgroup taxa (requires molecular clock) (-r) substitution_confidence (Switch) Estimate confidence intervals for rate of substitution (with +s option) (-is) date_confidence (Switch) Estimate confidence intervals for date of root of tree (with +s option) (-id) change_confidence (Switch) Estimate confidence intervals for rate of change of rate of substitution (with +w option) (-iw) limit (Float) Limit to use estimating confidence intervals (-l) codon_categories (String) CODON CATEGORIES = 112, 123, 120, etc. [default: homogeneity] (-p) codon_rate (String) CODON category rates: #1 #2 #3 separated by commas [default = estimate rates] (-c) seperate (Switch) Estimate seperate models for each site category (-e) gamma (Integer) Num categories for gamma rate heterogeneity (2 to 32) (-g) alpha (Integer) gamma shape (alpha) for site rate heterogeneity (-a) datasets (Integer) Number of Datasets (-n) user_branch (Switch) User branch-lengths [default = estimate] (-ul) treefile (InFile) Optional file containing trees equal_freq (Switch) Frequences of bases equal (-f=) freq_bases (String) Frequences of bases: #A #C #G #T separated by commas(-f) transition_transversion (Float) Transition/transversion ratio (-t) branch (Switch) Print final branch lengths (-vb) likelihoods (Switch) Write likelihoods for each Site (-vs) notrees (Switch) Don't Write trees (-vw) memory (Switch) Memory usage information (-vm) progress (Switch)

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

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