Manual Reference Pages - BIO::PHYLO::PARSERS::ADJACENCY (3)
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.
If you use Bio::Phylo in published research, please cite it:
<B>Rutger A VosB>, <B>Jason CaravasB>, <B>Klaas HartmannB>, <B>Mark A JensenB>
and <B>Chase MillerB>, 2011. Bio::Phylo - phyloinformatic analysis using Perl.
BMC Bioinformatics <B>12B>:63.
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