Markov Chain Models for Phylogenetic Trees
Estimate substitution rate matrix.
Estimate substitution rate matrix.
Markov chain models for phylogenetic trees.
Unique phyletic patterns with counts.
Plot the tree used with different hypothesized branch groupings (or cl...
Print summary information for the model fit.
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. See Dang and Golding (2016) <doi:10.1093/bioinformatics/btv541> for more details.