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Author image Rutger Vos
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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:


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