LineageSpecificSeqgen: generating sequence data with lineage-specific variation in the proportion of variable sites.

Abstract excerpt

BACKGROUND: Commonly used phylogenetic models assume a homogeneous evolutionary process throughout the tree. It is known that these homogeneous models are often too simplistic, and that with time some properties of the evolutionary process can change (due to selection or drift). In particular, as constraints on sequences evolve, the proportion of variable sites can vary between lineages. This affects the ability...

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