markophylo (Q136452)

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Markov Chain Models for Phylogenetic Trees
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markophylo
Markov Chain Models for Phylogenetic Trees

    Statements

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    1.0.8
    5 July 2020
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    1.0.1
    7 July 2015
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    1.0.2
    31 August 2015
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    1.0.3
    6 November 2015
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    1.0.4
    31 December 2015
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    1.0.6
    30 January 2018
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    1.0.7
    22 March 2019
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    1.0.9
    19 September 2023
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    19 September 2023
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    Allows for fitting of maximum likelihood models using Markov chains on phylogenetic trees for analysis of discrete character data. Examples of such discrete character data include restriction sites, gene family presence/absence, intron presence/absence, and gene family size data. Hypothesis-driven user- specified substitution rate matrices can be estimated. Allows for biologically realistic models combining constrained substitution rate matrices, site rate variation, site partitioning, branch-specific rates, allowing for non-stationary prior root probabilities, correcting for sampling bias, etc. See Dang and Golding (2016) <doi:10.1093/bioinformatics/btv541> for more details.
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