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Phylogenetic recombination detection is a fundamental task in bioinformatics and evolutionary biology. Most of the computational tools developed to attack this important problem are not integrated into the growing suite of R packages for statistical analysis of molecular sequences. Here, we present an R package, rbrothers, that makes a Bayesian multiple… (More)

Appendix A We present evidence supporting the claim that the stationary distribution of our new MCMC sampler is the posterior distribution, p(V, W|Y). This posterior has many aspects that could be examined, but for simplicity we focus on univariate statistics: the amount of time spent in each state and the number of transitions between each pair of states.… (More)

Phylogenetic stochastic mapping is a method for reconstructing the history of trait changes on a phylogenetic tree relating species/organism carrying the trait. State-of-the-art methods assume that the trait evolves according to a continuous-time Markov chain (CTMC) and works well for small state spaces. The computations slow down considerably for larger… (More)

- Jan Irvahn, Sujay Chattopadhyay, Evgeni V Sokurenko, Vladimir N Minin
- 2013

Phylogenetic recombination detection is a fundamental task in bioinformatics and evolutionary biology. Most of the computational tools developed to attack this important problem are not integrated into the growing suite of R packages for statistical analysis of molecular sequences. Here, we present an R package, rbrothers, that makes a Bayesian multiple… (More)

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