January 28, 2021 SaGePhy: A Phylogenetic Simulation Framework for Gene and Subgene Evolution by Soumya Kundu, University of Connecticut. Hosted by EvolCompGen COSI and SMBE
SaGePhy (pronounced sage-phy) is a software package for improved phylogenetic simulation of gene and subgene evolution. SaGePhy can be used to generate species trees, gene trees, and subgene or (protein) domain trees using a probabilistic birth–death process that allows for gene and subgene duplication, horizontal gene and subgene transfer, and gene and subgene loss. SaGePhy implements a range of important features not generally found in other phylogenetic simulation frameworks; these include the ability to simulate (i) subgene or domain level events inside one or more gene families, (ii) both additive and replacing horizontal gene and subgene/domain transfers, (iii) distance-biased horizontal transfers, and (iv) probabilistic sampling of species tree and gene tree nodes, respectively, for gene- and domain-family birth. SaGePhy therefore makes it possible to perform more realistic simulation of gene and subgene/domain evolution..