Department of Computer Science & Engineering, Storrs, CT, USA.
The Institute for Systems Genomics, University of Connecticut, Storrs, CT, USA.
Bioinformatics. 2019 Sep 15;35(18):3496-3498. doi: 10.1093/bioinformatics/btz081.
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- and domain-family birth. SaGePhy is open-source, platform independent and written in Java and Python.
Executables, source code (open-source under the revised BSD license) and a detailed manual are freely available from http://compbio.engr.uconn.edu/software/sagephy/.
Supplementary data are available at Bioinformatics online.
SaGePhy 是一个用于改进基因和亚基因进化系统发育模拟的软件包。SaGePhy 可以使用允许基因和亚基因复制、水平基因和亚基因转移以及基因和亚基因丢失的概率出生-死亡过程来生成种系树、基因树和亚基因或（蛋白质）结构域树。SaGePhy 实现了其他系统发育模拟框架/软件中没有的一系列重要功能。这些功能包括：（i）在一个或多个基因树内模拟亚基因或结构域水平的进化；（ii）同时模拟添加和替换水平基因/亚基因转移；（iii）基因和结构域家族发生时，分别对种系树和基因树节点进行概率抽样。SaGePhy 是开源的、独立于平台的，使用 Java 和 Python 编写。
可执行文件、源代码（根据修订后的 BSD 许可证开源）和详细手册可从 http://compbio.engr.uconn.edu/software/sagephy/ 免费获得。
补充数据可在生物信息学在线获得。
