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SIMMAP: Stochastic character mapping of discrete traits on phylogenies

BMC Bioinformatics · 2006 · Vol. 7(1) · pp. 88–88

Jonathan P. Bollback✉(University of Copenhagen)

Abstract

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.

Genomics and Phylogenetic Studies Genetic diversity and population structure Evolution and Genetic DynamicsCharacter (mathematics)Character evolutionBayesian probabilitySubstitution (logic)PhylogeneticsMaximum parsimonyBiologyProbabilistic logicEvolutionary biologyMarkov chain Monte Carlo

MeSH terms

AnimalsChromosome MappingComputer SimulationDNA Mutational AnalysisHumansModels, GeneticPhylogenySoftwareStochastic ProcessesUser-Computer InterfaceModels, StatisticalEvolution, MolecularQuantitative Trait Loci