Bio: : Phylo - phyloinformatic analysis using Perl

Background: Phyloinformatic analyses involve large amounts of data and metadata of complex structure. Collecting, processing, analyzing, visualizing and summarizing these data and metadata should be done in steps that can be automated and reproduced. This requires flexible, modular toolkits that can represent, manipulate and persist phylogenetic data and metadata as objects with programmable interfaces. Results: This paper presents Bio::Phylo, a Perl5 toolkit for phyloinformatic analysis. It implements classes and methods that are compatible with the well-known BioPerl toolkit, but is independent from it (making it easy to install) and features a richer API and a data model that is better able to manage the complex relationships between different fundamental data and metadata objects in phylogenetics. It supports commonly used file formats for phylogenetic data including the novel NeXML standard, which allows rich annotations of phylogenetic data to be stored and shared. Bio::Phylo ca...

• Type: Journal
• Year: 2011
• Where: BMCBI
• Authors: Rutger A. Vos, Jason Caravas, Klaas Hartmann, Mark A. Jensen, Chase Miller
• Keywords: Artificial Intelligence, BMCBI 2011, Character State, Metadata, Phylogenetic Data