Package: markophylo
Type: Package
Title: Markov Chain Models for Phylogenetic Trees
Version: 1.0.1
Date: 2015-07-06
Author: Utkarsh J. Dang and G. Brian Golding
Maintainer: Utkarsh J. Dang <udang@mcmaster.ca>
Description: 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. 
License: GPL (>= 2)
Imports: Rcpp (>= 0.11.4)
LinkingTo: Rcpp, RcppArmadillo
Suggests: ape (>= 3.2), stringr (>= 0.6.2), numDeriv (>= 2012.9.1),
        phangorn (>= 1.99.13), knitr (>= 1.10)
Depends: R (>= 2.10)
VignetteBuilder: knitr
LazyData: true
NeedsCompilation: yes
Packaged: 2015-07-07 15:09:14 UTC; owner
Repository: CRAN
Date/Publication: 2015-07-07 18:10:58
