SYNOPSIS

use base qw(Bio::Tools::Run::Phylo::PhyloBase);

DESCRIPTION

For use by Bio::Tools::Run::Phylo modules as a base in place of Bio::Tools::Run::WrapperBase.

This is based on WrapperBase but provides additional phylo-related private helper subs.

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.

  [email protected]                  - General discussion
  http://bioperl.org/wiki/Mailing_lists  - About the mailing lists

Support

Please direct usage questions or support issues to the mailing list:

[email protected]

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:

  http://redmine.open-bio.org/projects/bioperl/

AUTHOR - Sendu Bala

Email [email protected]

APPENDIX

The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _

_alignment

 Title   : _alignment
 Usage   : $aln = $obj->_alignment()
 Function: Get/set an alignment object, generating one from a file if desired.
 Returns : Bio::Align::AlignI (probably a Bio::SimpleAlign)
 Args    : none to get
           OR filename & input format of the alignment file (latter defaults to
           guess) to set from file
           OR Bio::Align::AlignI to set

_write_alignment

 Title   : _write_alignment
 Usage   : $obj->_write_alignment()
 Function: Writes the alignment object returned by _alignment() out in the
           desired format to a temp file.
 Returns : filename
 Args    : string to desribe format (default 'fasta'), any other options to pass
           to AlignIO

_tree

 Title   : _tree
 Usage   : $tree = $obj->_tree()
 Function: Get/set a tree object, generating one from a file/database if desired
 Returns : Bio::Tree::TreeI
 Args    : none to get, OR to set:
           OR filename & input format of the tree file (latter defaults to
           guess) to set from file
           OR Bio::Tree::TreeI
           OR Bio::DB::Taxonomy when _alignment() has been set and where
           sequences in the alignment have ids matching species in the taxonomy
           database

_write_tree

 Title   : _write_tree
 Usage   : $obj->_write_tree()
 Function: Writes the tree object returned by _tree() out in the desired format
           to a temp file.
 Returns : filename
 Args    : string to desribe format (default 'newick')

_get_seq_names

 Title   : _get_seq_names
 Usage   : @names = $obj->_get_seq_names()
 Function: Get all the sequence names (from id()) of the sequenes in the
           alignment.  _alignment() must be set prior to calling this.
 Returns : list of strings (seq ids)
 Args    : none

_get_node_names

 Title   : _get_node_names
 Usage   : @names = $obj->_get_node_names()
 Function: Get all the node names (from id()) of the nodes in the tree.
           _tree must be set prior to calling this.
 Returns : list of strings (node ids)
 Args    : none

_check_names

 Title   : _check_names
 Usage   : if ($obj->_check_names) { ... }
 Function: Determine if all sequences in the alignment file have a corresponding
           node in the tree file. _alignment() and _tree() must be set
           prior to calling this.
 Returns : boolean (will also warn about the specific problems when returning
           false)
 Args    : none