Models for Similarity Distributions of Syntenic Homologs and Applications to Phylogenomics

David Sankoff, Chunfang Zheng, Yue Zhang, João Meidanis, Eric Lyons, Haibao Tang

Research output: Contribution to journalArticlepeer-review

5 Scopus citations

Abstract

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.

Original languageEnglish (US)
Article number8423659
Pages (from-to)727-737
Number of pages11
JournalIEEE/ACM Transactions on Computational Biology and Bioinformatics
Volume16
Issue number3
DOIs
StatePublished - May 1 2019

Keywords

  • Brassicaceae
  • Gene tree
  • algorithms
  • mixture of distributions
  • species tree
  • whole genome doubling

ASJC Scopus subject areas

  • Biotechnology
  • Genetics
  • Applied Mathematics

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