Bio::Phylo::Parsers::Adjacency - Parser used by Bio::Phylo::IO, no serviceable parts inside
This module parses a tree structure from tabular data organized as an "adjacency list", i.e. child -> parent relationships. The table should at least have the following columns: 'child' and 'parent'. 'length' is interpreted as branch length. Columns starting with 'node:' are assigned as semantic annotations to the focal node, columns starting with 'branch:' are assigned to the focal branch. Records need to be listed in pre-order, so that references to parent nodes can be resolved immediately. Consequently, the root is the first record, without a parent. Example:
((A:1,B:2)n1:3,C:4)n2:0;
Becomes (with an extra example annotation):
child parent length node:dcterms:identifier n2 0 35462 n1 n2 3 34987 A n1 1 73843 B n1 2 98743 C n2 4 39847
There is a mailing list at https://groups.google.com/forum/#!forum/bio-phylo for any user or developer questions and discussions.
The adjacency parser is called by the Bio::Phylo::IO object. Look there to learn how to parse trees in general
Also see the manual: Bio::Phylo::Manual and http://rutgervos.blogspot.com
If you use Bio::Phylo in published research, please cite it:
Rutger A Vos, Jason Caravas, Klaas Hartmann, Mark A Jensen and Chase Miller, 2011. Bio::Phylo - phyloinformatic analysis using Perl. BMC Bioinformatics 12:63. http://dx.doi.org/10.1186/1471-2105-12-63
To install Bio::Phylo, copy and paste the appropriate command in to your terminal.
cpanm
cpanm Bio::Phylo
CPAN shell
perl -MCPAN -e shell install Bio::Phylo
For more information on module installation, please visit the detailed CPAN module installation guide.