Generating Heterogeneous Data on Gene Trees

We introduce GenPhylo, a Python module that simulates nucleotide sequence data along a phylogeny avoiding the restriction of continuous-time Markov processes. GenPhylo uses directly a general Markov model and therefore naturally incorporates heterogeneity across lineages. We solve the challenge of generating transition matrices with a pre-given expected number of substitutions (the branch length information) by providing an algorithm that can be incorporated in other simulation software.