NGS-MC is an R package which calculates the statistics and estimators in a Markov sequence model including the effective coverage, a chi-square statistic for k-words, normal approximation for every k-word, and five estimators for the order of Markov chain from NGS short read data.
BEAST (Bayesian Evolutionary Analysis Samling Trees) is a cross-platform program for Bayesian MCMC analysis of molecular sequences. It is entirely orientated towards rooted, time-measured phylogenies inferred using strict or relaxed molecular clock models. It can be used as a method of reconstructing phylogenies but is also a framework for testing evolutionary hypotheses without conditioning on a single tree topology. BEAST uses MCMC to average over tree space, so that each tree is weighted proportional to its posterior probability. We include a simple to use user-interface program for setting up standard analyses and a suit of programs for analysing the results.
BEAST 2 is an open source cross-platform program for Bayesian MCMC phylogenetic analysis of molecular sequences.
BEAST 2.5: An advanced software platform for Bayesian evolutionary analysis.
Bouckaert R, Vaughan TG, Barido-Sottani J, Duchêne S, Fourment M, Gavryushkina A, Heled J, Jones G, Kühnert D, De Maio N, Matschiner M, Mendes FK, Müller NF, Ogilvie HA, du Plessis L, Popinga A, Rambaut A, Rasmussen D, Siveroni I, Suchard MA, Wu CH, Xie D, Zhang C, Stadler T, Drummond AJ.
PLoS Comput Biol. 2019 Apr 8;15(4):e1006650. doi: 10.1371/journal.pcbi.1006650.
GARLI (Genetic Algorithm for Rapid Likelihood Inference) performs phylogenetic searches on aligned nucleotide, codon and amino acid data sets using the maximum likelihood criterion. On a practical level, the program is able to perform maximum-likelihood tree searches on large data sets in a number of hours.