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://github.com/bioperl/bioperl-live/issues

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 minimum taxon name length
 Returns : integer (length of name)
 Args    : integer