Query: bio::treeio::pag
OS: debian
Section: 3pm
Format: Original Unix Latex Style Formatted with HTML and a Horizontal Scroll Bar
Bio::TreeIO::pag(3pm) User Contributed Perl Documentation Bio::TreeIO::pag(3pm)NAMEBio::TreeIO::pag - Bio::TreeIO driver for Pagel formatSYNOPSISuse 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); }DESCRIPTIONConvert a Bio::TreeIO to Pagel format. More information here http://www.evolution.reading.ac.uk/index.htmlFEEDBACKMailing 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-orgAPPENDIXThe 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)
Similar Topics in the Unix Linux Community |
---|
Introduction |
One instance of comparing grep and awk |
Find columns in a file based on header and print to new file |
New UNIX and Linux History Sections |