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Tools to better understand biology by tapping information in phylogenies 		Not logged in

SIMMAP 1.0: SIMMAP is a post tree analysis software package for stochastically mapping characters (mutations) on phylogenies. It uses an \"indirect\" approach as first developed by Nielsen (2002). The name SIMMAP is an acronym for StochastIc Mutational MApping on Phylogenies. SIMMAP has been developed to implement stochastic character mapping that is useful to molecular evolutionists, systematists, and bioinformaticians. Stochastic mutational 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 are accommodated by using Markov chain Monte Carlo (MCMC) samples from their respective posterior distributions. Researchers can address questions about positive selection, patterns of amino acid substitution, character association, and patterns of morphological evolution.


Cost: $0


Open source: no


URL: http://www.simmap.com/v1.0/simmap.html


Citations(s) (based on web hits only through time [why]):

Citation chart


Reference(s):

Jonathan P Bollback 2006 "SIMMAP: Stochastic character mapping of discrete traits on phylogenies" BMC Bioinformatics 7(1): 88-88


Data formats :

  • NEXUS


Tree formats :

  • NEXUS


Methods and character types :

  • Stochastic character mapping
    DNA strict
    RNA strict
    AA strict
    Binary
    Multistate unordered
    DNA strict-DNA strict
    DNA strict-RNA strict
    DNA strict-AA strict
    DNA strict-Binary
    DNA strict-Multistate unordered
    RNA strict-DNA strict
    RNA strict-RNA strict
    RNA strict-AA strict
    RNA strict-Binary
    RNA strict-Multistate unordered
    AA strict-DNA strict
    AA strict-RNA strict
    AA strict-AA strict
    AA strict-Binary
    AA strict-Multistate unordered
    Binary-Binary
    Binary-Multistate unordered
    Multistate unordered-DNA strict
    Multistate unordered-RNA strict
    Multistate unordered-AA strict
    Multistate unordered-Binary
    Multistate unordered-Multistate unordered


Application kind and platform :

  • standalone application with GUI: Mac OS 10.3, Mac OS 10.4, Mac OS 10.5
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