Bio::TreeIO::pag - Bio::TreeIO driver for Pagel format
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); }
Convert a Bio::TreeIO to Pagel format. More information here http://sapc34.rdg.ac.uk/meade/Mark/
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The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
Title : new Usage : my $obj = new Bio::TreeIO::pag(); Function: Builds a new Bio::TreeIO::pag object Returns : an instance of Bio::TreeIO::pag Args : -file/-fh for filename or filehandles
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
Title : next_tree Usage : Function: Example : Returns : Args :
To install Bio::Seq, copy and paste the appropriate command in to your terminal.
cpanm
cpanm Bio::Seq
CPAN shell
perl -MCPAN -e shell install Bio::Seq
For more information on module installation, please visit the detailed CPAN module installation guide.