GenPhyloData: realistic simulation of gene family evolution
PrIME-GenPhyloData is a suite of tools for creating realistic simulated phylogenetic trees, in particular for families of homologous genes. It supports generation of trees based on a birth-death process andperhaps more interestinglyalso supports generation of gene family trees guided by a known (synthetic or biological) species tree while accounting for events such as gene duplication, gene loss, and lateral gene transfer (LGT). The suite also supports a wide range of branch rate models enabling relaxation of the molecular clock.
gene family phylogenetics gene duplication gene loss lgt molecular clock synthetic data biogeography host-parasite co-evolution