markophylo: Markov Chain Models for Phylogenetic Trees

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.

Version: 1.0.4
Depends: R (≥ 2.10)
Imports: Rcpp (≥ 0.11.4), ape (≥ 3.2), numDeriv (≥ 2012.9.1), phangorn (≥ 1.99.13)
LinkingTo: Rcpp, RcppArmadillo
Suggests: knitr (≥ 1.10), testthat (≥ 0.9.1)
Published: 2015-12-31
Author: Utkarsh J. Dang and G. Brian Golding
Maintainer: Utkarsh J. Dang <udang at>
License: GPL-2 | GPL-3 [expanded from: GPL (≥ 2)]
NeedsCompilation: yes
Citation: markophylo citation info
Materials: NEWS
In views: Phylogenetics
CRAN checks: markophylo results


Reference manual: markophylo.pdf
Vignettes: Markov Chain Analysis on Phylogenetic Trees
Package source: markophylo_1.0.4.tar.gz
Windows binaries: r-devel:, r-release:, r-oldrel:
OS X El Capitan binaries: r-release: markophylo_1.0.4.tgz
OS X Mavericks binaries: r-oldrel: markophylo_1.0.4.tgz
Old sources: markophylo archive


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