Bio::NEXUS: a Perl API for the NEXUS format for comparative biological data |
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| Authors: | Thomas Hladish Vivek Gopalan Chengzhi Liang Weigang Qiu Peter Yang Arlin Stoltzfus |
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| Affiliation: | (1) Center for Advanced Research in Biotechnology, 9600 Gudelsky Drive, Rockville, MD 20850, USA;(2) Section of Integrative Biology, University of Texas at Austin, 1 University Station C0930, Austin, Texas 78712, USA;(3) Cold Spring Harbor Laboratory, , 1 Bungtown Rd, Cold Spring Harbor, NY 11724, USA;(4) Department of Biological Sciences, Hunter College, CUNY, 695 Park Ave., New York, NY 10021, USA;(5) Biochemical Science Division, National Institute of Standards and Technology, Gaithersburg, MD 20899-8310, USA |
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| Abstract: | 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. |
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