Developers: Vladimir Minin, John O'Brien, and Marc Suchard
Maintainer: Vladimir Minin,
Overview: markovjumps provides routines for calculation of properties of continuous-time Markov chain-induced counting processes and reward processes. We tailored these caclulations for molecular evolution applications, such as simulation-free stochastic mapping and robust estimation of evolutionary distances (see references below).
Source code: markovjumps.tar.gz
Installation: brief instructions
Tutorials:
- Tutorial I: Nucleotide labeled distances
- Tutorial II: Codon labeled distances (synonymous/nonsynonymous)
- Minin VN and Suchard MA.
Counting labeled transitions in continuous-time
Markov models of evolution,
Journal of Mathematical Biology, 56:391-412, 2008.
- Minin VN and Suchard MA.
Fast, accurate and simulation-free stochastic mapping,
Philosophical Transactions of the Royal Society B: Biological Sciences,
363:3985-3995, 2008.
- O'Brien JD, Minin VN, and Suchard MA.
Learning to count: robust estimates for labeled distances between
molecular sequences,
Molecular Biology and Evolution, 26:801-814, 2009.