| Bio::TreeIO::pag(3pm) | User Contributed Perl Documentation | Bio::TreeIO::pag(3pm) |
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://www.evolution.reading.ac.uk/index.html
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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 = 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)
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 :
Title : name_length Usage : $self->name_length(20); Function: set minimum taxon name length Returns : integer (length of name) Args : integer
| 2021-08-15 | perl v5.32.1 |