Bio: : NEXUS: a Perl API for the NEXUS format for comparative biological data

Background: Evolutionary analysis provides a formal framework for comparative analysis of genomic and other data. In evolutionary analysis, observed data are treated as the terminal states of characters that have evolved (via transitions between states) along the branches of a tree. The NEXUS standard of Maddison, et al. (1997; Syst. Biol. 46: 590–621) provides a portable, expressive and flexible text format for representing character-state data and trees. However, due to its complexity, NEXUS is not well supported by software and is not easily accessible to bioinformatics users and developers. Results: Bio::NEXUS is an application programming interface (API) implemented in Perl, available from CPAN and SourceForge. The 22 Bio::NEXUS modules define 351 methods in 4229 lines of code, with 2706 lines of POD (Plain Old Documentation). Bio::NEXUS provides an object-oriented interface to reading, writing and manipulating the contents of NEXUS files. It closely follows the extensive expla...

• Type: Journal
• Year: 2007
• Where: BMCBI
• Authors: Thomas Hladish, Vivek Gopalan, Chengzhi Liang, Wei-Gang Qiu, Peter Yang, Arlin Stoltzfus
• Keywords: BMCBI 2007, Comparative Analysis, Et Al, Evolutionary Analysis