NAME
Bio::Tools::Run::PiseApplication::protpars
SYNOPSIS
#DESCRIPTION
Bio::Tools::Run::PiseApplication::protpars
Bioperl class for:
Phylip protpars - Protein Sequence Parcimony Method (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/protpars.html
for available values):
protpars (String)
infile (Sequence)
Alignement File
pipe: readseq_ok_alig
use_threshold (Switch)
Use Threshold parsimony (T)
threshold (Integer)
Threshold value (if use threshold parsimony)
code (Excl)
Genetic code (U)
jumble (Switch)
Randomize (jumble) input order of sequences (J)
jumble_seed (Integer)
Jumble random number seed (must be odd)
times (Integer)
Number of times to jumble
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
consense (Switch)
Compute a consensus tree
user_tree (Switch)
Use User tree (default: no, search for best tree) (U)
tree_file (InFile)
User Tree file
print_tree (Switch)
Print out tree (3)
print_sequences (Switch)
Print sequences at all nodes of tree (5)
print_treefile (Switch)
Write out trees onto tree file (6)
printdata (Switch)
Print out the data at start of run (1)
print_steps (Switch)
Print out steps in each site (4)
indent_tree (Switch)
Indent treefile
outgroup (Integer)
Outgroup species (default, use as outgroup species 1) (O)
confirm (String)
terminal_type (String)
multiple_dataset (String)
bootconfirm (String)
bootterminal_type (String)
consense_confirm (String)
consense_terminal_type (String)
consense_outgroup (String)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/MailList.shtml - About the mailing listsReporting 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 email or the web:
bioperl-bugs@bioperl.org
http://bioperl.org/bioperl-bugs/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/protpars.html
Bio::Tools::Run::PiseApplication
Bio::Tools::Run::AnalysisFactory::Pise
Bio::Tools::Run::PiseJob
new
Title : new()
Usage : my $protpars = Bio::Tools::Run::PiseApplication::protpars->new($location, $email, @params);
Function: Creates a Bio::Tools::Run::PiseApplication::protpars 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 $protpars = $factory->program('protpars');
Example : -
Returns : An instance of Bio::Tools::Run::PiseApplication::protpars.