SaGePhy: An improved phylogenetic simulation framework for gene and subgene evolution.

Summary: SaGePhy 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 found in other phylogenetic simulation frameworks/software. These include (i) simulation of subgene or domain level evolution inside one or more gene trees, (ii) simultaneous simulation of both additive and replacing horizontal gene/subgene transfers, and (iii) probabilistic sampling of species tree and gene tree nodes, respectively, for gene-family and domain-family birth. SaGePhy is open-source, platform independent, and written in Java and Python.

Availability: Executables, source code (open-source under the revised BSD licence), and a detailed manual are freely available from https://compbio.engr.uconn.edu/software/sagephy/.