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.


CONCLUSIONS
Stochastic character mapping, as implemented in the SIMMAP software, enables users to address questions that require mapping characters onto phylogenies using a probabilistic approach that does not rely on parsimony. Analyses can be performed using a fully Bayesian approach that is not reliant on considering a single topology, set of substitution model parameters, or reconstruction of ancestral states. Uncertainty in these quantities is accommodated by using MCMC samples from their respective posterior distributions.
Bollback
Jonathan P
JP
Bioinformatics Center, University of Copenhagen, Universitetsparken 15, Building 10, 2100 Copenhagen Ø, Denmark. bollback@binf.ku.dk
D000818:Animals; D002874:Chromosome Mapping / Q000379:methods*; D003198:Computer Simulation; D004252:DNA Mutational Analysis / Q000379:methods*; D019143:Evolution, Molecular; D006801:Humans; D008957:Models, Genetic; D015233:Models, Statistical; D010802:Phylogeny; D040641:Quantitative Trait Loci / Q000235:genetics*; D012984:Software; D013269:Stochastic Processes; D014584:User-Computer Interface