SIMMAP: Stochastic character mapping of discrete traits on phylogenies

Background: Character mapping on phylogenies has played an important, if not critical role, in our understanding of molecular, morphological, and behavioral evolution. Until very recently we have relied on parsimony to infer character changes. Parsimony has a number of serious limitations that are drawbacks to our understanding. Recent statistical methods have been developed that free us from these limitations enabling us to overcome the problems of parsimony by accommodating uncertainty in evolutionary time, ancestral states, and the phylogeny. Results: SIMMAP has been developed to implement stochastic character mapping that is useful to both molecular evolutionists, systematists, and bioinformaticians. Researchers can address questions about positive selection, patterns of amino acid substitution, character association, and patterns of morphological evolution. Conclusion: Stochastic character mapping, as implemented in the SIMMAP software, enables users to address questions that req...

• Type: Journal
• Year: 2006
• Where: BMCBI
• Authors: Jonathan P. Bollback
• Keywords: BMCBI 2006, Character Change, Parsimony, Stochastic Character Mapping