Joachim Bargsten > Bio-Gonzales > Bio::Gonzales::Phylo::Util

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Module Version: 0.0547   Source   Latest Release: Bio-Gonzales-0.0547_01

NAME ^

Bio::Gonzales::Phylo::Util - utility functions for phylogenetic analysis

SYNOPSIS ^

    use Bio::Gonzales::Phylo::Util qw(leaf_mapper consensus_tree);

DESCRIPTION ^

SUBROUTINES ^

$map_iterator = leaf_mapper($code_ref // $pattern_or_map // '%s09d')

Example for a code reference:

    my $map;
    my $handler = sub {
        my ($id) = @_;
        
        return $map->{$id} // $id . '.NA';
    };

    my $map_iterator = leaf_mapper($handler);

    my $mapped_tree = $map_iterator->($tree);

The iterator takes a Bio::Phylo::Forest::Tree object and remaps it. The mapping takes place directly on the tree, thus alters it.

consensus_tree($input_trees_file, $consensus_tree_file)

Parses the $input_tree_file, builds a consensus tree and writes it to $consensus_tree_file.

SEE ALSO ^

AUTHOR ^

jw bargsten, <joachim.bargsten at wur.nl>

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