Models for Similarity Distributions of Syntenic Homologs and Applications to Phylogenomics

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

Research output: Contribution to journalArticle

4 Scopus citations

Abstract

We outline an integrated approach to speciation and whole genome duplication (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)
JournalIEEE/ACM Transactions on Computational Biology and Bioinformatics
DOIs
StateAccepted/In press - Jul 30 2018

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Keywords

  • algorithms
  • Analytical models
  • Bioinformatics
  • Biological system modeling
  • Brassicaceae
  • Computational modeling
  • Fractionation
  • Gaussian distribution
  • gene tree
  • Genomics
  • mixture of distributions
  • species tree
  • whole genome doubling

ASJC Scopus subject areas

  • Biotechnology
  • Genetics
  • Applied Mathematics

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