Bio::TreeIO::pag(3pm) User Contributed Perl Documentation Bio::TreeIO::pag(3pm)
NAME
Bio::TreeIO::pag - Bio::TreeIO driver for Pagel format
SYNOPSIS
use Bio::TreeIO;
my $in = Bio::TreeIO->new(-format => 'nexus',
-file => 't/data/adh.mb_tree.nexus');
my $out = Bio::TreeIO->new(-format => 'pag');
while( my $tree = $in->next_tree ) {
$out->write_tree($tree);
}
DESCRIPTION
Convert a Bio::TreeIO to Pagel format. More information here http://www.evolution.reading.ac.uk/index.html
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/wiki/Mailing_lists - About the mailing lists
Support
Please direct usage questions or support issues to the mailing list:
bioperl-l@bioperl.org
rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address
it. Please include a thorough description of the problem with code and data examples if at all possible.
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:
https://redmine.open-bio.org/projects/bioperl/
AUTHOR - Jason Stajich
Email jason-at-bioperl-dot-org
APPENDIX
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
new
Title : new
Usage : my $obj = Bio::TreeIO::pag->new();
Function: Builds a new Bio::TreeIO::pag object
Returns : an instance of Bio::TreeIO::pag
Args : -file/-fh for filename or filehandles
-name_length for minimum name length (default = 10)
write_tree
Title : write_tree
Usage :
Function: Write a tree out in Pagel format
Some options are only appropriate for bayesianmultistate and
the simpler output is only proper for discrete
Returns : none
Args : -no_outgroups => (number)
-print_header => 0/1 (leave 0 for discrete, 1 for bayesianms)
-special_node => special node - not sure what they wanted to do here
-keep_outgroup => 0/1 (keep the outgroup node in the output)
-outgroup_ancestor => Bio::Tree::Node (if we want to exclude or include the outgroup this is what we operate on)
-tree_no => a tree number label - only useful for BayesianMultistate
next_tree
Title : next_tree
Usage :
Function:
Example :
Returns :
Args :
name_length
Title : name_length
Usage : $self->name_length(20);
Function: set mininum taxon name length
Returns : integer (length of name)
Args : integer
perl v5.14.2 2012-03-02 Bio::TreeIO::pag(3pm)