NAME

       Bio::Tools::Run::Phylo::PhyloBase- base module for phylo wrappers

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.

         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:

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

AUTHOR - Sendu Bala

       Email bix@sendu.me.uk

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 describe 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 describe 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