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30 Oct 2017 19:50:35 UTC
- Distribution: Bio-Phylo
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Bus factor: 1- 56.90% Coverage
- License: perl_5
- Perl: v5.8.0
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NAME
Bio::Phylo::Unparsers::Adjacency - Serializer used by Bio::Phylo::IO, no serviceable parts inside
DESCRIPTION
This module turns a tree structure into tabular data organized as an "adjacency list", i.e. child -> parent relationships. The table at least has the following columns: 'child' and 'parent'. 'length' is interpreted as branch length. Columns starting with 'node:' are created for semantic annotations to the focal node, columns starting with 'branch:' are created for the focal branch. Records are 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
SEE ALSO
There is a mailing list at https://groups.google.com/forum/#!forum/bio-phylo for any user or developer questions and discussions.
- Bio::Phylo::IO
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The adjacency unparser is called by the Bio::Phylo::IO object. Look there to learn how to unparse trees.
- Bio::Phylo::Manual
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Also see the manual: Bio::Phylo::Manual and http://rutgervos.blogspot.com.
CITATION
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
Module Install Instructions
To install Bio::Phylo, copy and paste the appropriate command in to your terminal.
cpanm Bio::Phylo
perl -MCPAN -e shell install Bio::Phylo
For more information on module installation, please visit the detailed CPAN module installation guide.