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arXiv · 2504.15855

Generating heterogeneous data on gene trees

Martí Cortada Garcia·Adrià Diéguez Moscardó·Marta Casanellas
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Abstract

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.

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Martí Cortada Garcia, Adrià Diéguez Moscardó, Marta Casanellas. 2025-04-22. Generating heterogeneous data on gene trees. https://arxiv.org/abs/2504.15855

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