title: An update of DIVERGE software for functional divergence analysis of protein family.
abstract: DIVERGE is a software system for phylogeny-based analyses of protein family evolution and functional divergence. It provides a suite of statistical tools for selection and prioritization of the amino acid sites that are responsible for the functional divergence of a gene family. The synergistic efforts of DIVERGE and other methods have convincingly demonstrated that the pattern of rate change at a particular amino acid site may contain insightful information about the underlying functional divergence following gene duplication. These predicted sites may be used as candidates for further experiments. We are now releasing an updated version of DIVERGE with the following improvements: 1) a feasible approach to examining functional divergence in nearly complete sequences by including deletions and insertions (indels); 2) the calculation of the false discovery rate of functionally diverging sites; 3) estimation of the effective number of functional divergence-related sites that is reliable and insensitive to cutoffs; 4) a statistical test for asymmetric functional divergence; and 5) a new method to infer functional divergence specific to a given duplicate cluster. In addition, we have made efforts to improve software design and produce a well-written software manual for the general user.
authors.affiliation: State Key Laboratory of Genetic Engineering and MOE Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai, China. xgu@iastate.edu
authors.forename: Xun
authors.initials: X
authors.lastname: Gu
authors.forename: Yangyun
authors.initials: Y
authors.lastname: Zou
authors.forename: Zhixi
authors.initials: Z
authors.lastname: Su
authors.forename: Wei
authors.initials: W
authors.lastname: Huang
authors.forename: Zhan
authors.initials: Z
authors.lastname: Zhou
authors.forename: Zebulun
authors.initials: Z
authors.lastname: Arendsee
authors.forename: Yanwu
authors.initials: Y
authors.lastname: Zeng
mesh_terms: D000595:Amino Acid Sequence; D000596:Amino Acids / Q000235:genetics*; D000818:Animals; D019143:Evolution, Molecular; D020440:Gene Duplication; D054643:INDEL Mutation; D008957:Models, Genetic; D005810:Multigene Family; D010802:Phylogeny; D011506:Proteins / Q000145:classification / Q000235:genetics*; D012984:Software; D014714:Vertebrates / Q000235:genetics
chemical_list: D000596:Amino Acids; D011506:Proteins
keywords: DIVERGE; gene duplication; gene family evolution; type I functional divergence; type II functional divergence