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.

Install the latest version of this package by entering the following in R:
install.packages("markophylo")
AuthorUtkarsh J. Dang and G. Brian Golding
Date of publication2015-12-31 08:29:14
MaintainerUtkarsh J. Dang <udang@mcmaster.ca>
LicenseGPL (>= 2)
Version1.0.4

View on CRAN

Files

inst
inst/CITATION
inst/doc
inst/doc/estimaterates.R
inst/doc/estimaterates.html
inst/doc/estimaterates.Rmd
tests
tests/testthat.R
tests/testthat
tests/testthat/test-main.R
src
src/Makevars
src/loopC-general4.cpp
src/Makevars.win
src/RcppExports.cpp
NAMESPACE
NEWS
data
data/simdata5.rda
data/simdata4.rda
data/simdata2.rda
data/simdata1.rda
data/simdata3.rda
R
R/custom-general14.R R/RcppExports.R
vignettes
vignettes/estimaterates.Rmd
MD5
build
build/vignette.rds
DESCRIPTION
man
man/plottree.Rd man/estimaterates.Rd man/print.markophylo.Rd man/markophylo-package.Rd man/simdata1.Rd man/patterns.Rd

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

Please suggest features or report bugs with the GitHub issue tracker.

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