Models for Similarity Distributions of Syntenic Homologs and Applications to Phylogenomics

被引：10

作者：

Sankoff, David ^{[1
]}

Zheng, Chunfang ^{[1
]}

Zhang, Yue ^{[1
]}

Meidanis, Joao ^{[1
]}

Lyons, Eric ^{[2
]}

Tang, Haibao ^{[2
]}

机构：

[1] Univ Ottawa, Dept Math & Stat, Ottawa, ON K1N 6N5, Canada

[2] Univ Arizona, Sch Plant Sci, Tucson, AZ 85721 USA

来源：

IEEE-ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS | 2019年 / 16卷 / 03期

基金：

巴西圣保罗研究基金会; 加拿大自然科学与工程研究理事会;

关键词：

Gene tree; species tree; whole genome doubling; algorithms; mixture of distributions; Brassicaceae; GENOME EVOLUTION; PROVIDES INSIGHT; CONSEQUENCES; BRASSICACEAE; ARABIDOPSIS; SEQUENCES;

D O I：

10.1109/TCBB.2018.2849377

中图分类号：

Q5 [生物化学];

学科分类号：

071010 ; 081704 ;

摘要：

We outline an integrated approach to speciation and whole genome doubling (WGD) to resolve the occurrence of these events in phylogenetic analysis. We propose a more principled way of estimating the parameters of gene divergence and fractionation than the standard mixture of normals analysis. We formulate an algorithm for resolving data on local peaks in the distributions of duplicate gene similarities for a number of related genomes. We illustrate with a comprehensive analysis of WGD-origin duplicate gene data from the family Brassicaceae.

引用

页码：727 / 737

页数：11

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