TAXODIUM version 1.0: a simple way to generate uniform and fractionally weighted three-item matrices from various kinds of biological data

An open-access program for generating three-item statement (3TS) matrices from data such as molecular sequences does not currently exist. The recently developed LisBeth package allows for representation of hypotheses of homology among taxa or areas directly as rooted trees or as hierarchies; however...

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Bibliographic Details
Published in:PloS one 2012-11, Vol.7 (11), p.e48813-e48813
Main Authors: Mavrodiev, Evgeny V, Madorsky, Alexander
Format: Article
Language:English
Subjects:
Biogeography
Biology
C plus plus
Computational Biology - methods
Computer Science
Databases as Topic
DNA - genetics
Exploration
Hierarchies
Homology
Hypotheses
Phylogenetics
Software
Statistical analysis
Taxa
Trees
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Summary:An open-access program for generating three-item statement (3TS) matrices from data such as molecular sequences does not currently exist. The recently developed LisBeth package allows for representation of hypotheses of homology among taxa or areas directly as rooted trees or as hierarchies; however, LisBeth is not a standard matrix-based platform. Here we present "TAXODIUM version 1.0" (TAXODIUM), a program designed for building 3TS-matrices from binary, additive (ordered) and non-additive (unordered) multistate characters, with both uniform and fractional weighting of the statements. TAXODIUM also facilitates, for the first time, use of Maximum Likelihood analyses with 3TS matrices, but future implementation of the 3TS analysis in a statistical framework will require more exploration.
ISSN:1932-6203
1932-6203
DOI:10.1371/journal.pone.0048813