Models for Similarity Distributions of Syntenic Homologs and Applications to Phylogenomics

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

doi:10.1109/TCBB.2018.2849377

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 journal › Article › peer-review

11 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 language	English (US)
Article number	8423659
Pages (from-to)	727-737
Number of pages	11
Journal	IEEE/ACM Transactions on Computational Biology and Bioinformatics
Volume	16
Issue number	3
DOIs	https://doi.org/10.1109/TCBB.2018.2849377
State	Published - 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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10.1109/TCBB.2018.2849377

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AU - Zheng, Chunfang

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AU - Meidanis, João

AU - Lyons, Eric

AU - Tang, Haibao

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AB - 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.

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KW - Gene tree

KW - algorithms

KW - mixture of distributions

KW - species tree

KW - whole genome doubling

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Models for Similarity Distributions of Syntenic Homologs and Applications to Phylogenomics

Abstract

Keywords

ASJC Scopus subject areas

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