Ortholog-Finder: A Tool for Constructing an Ortholog Data Set

Genome Biology and Evolution
Tokumasa HoriikeYoshio Tateno

Abstract

Orthologs are widely used for phylogenetic analysis of species; however, identifying genuine orthologs among distantly related species is challenging, because genes obtained through horizontal gene transfer (HGT) and out-paralogs derived from gene duplication before speciation are often present among the predicted orthologs. We developed a program, "Ortholog-Finder," to obtain ortholog data sets for performing phylogenetic analysis by using all open-reading frame data of species. The program includes five processes for minimizing the effects of HGT and out-paralogs in phylogeny construction: 1) HGT filtering: Genes derived from HGT could be detected and deleted from the initial sequence data set by examining their base compositions. 2) Out-paralog filtering: Out-paralogs are detected and deleted from the data set based on sequence similarity. 3) Classification of phylogenetic trees: Phylogenetic trees generated for ortholog candidates are classified as monophyletic or polyphyletic trees. 4) Tree splitting: Polyphyletic trees are bisected to obtain monophyletic trees and remove HGT genes and out-paralogs. 5) Threshold changing: Out-paralogs are further excluded from the data set based on the difference in the similarity scores o...Continue Reading

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Citations

Jan 29, 2020·The New Phytologist·Jarrett ManMadelaine Bartlett
Nov 23, 2017·Frontiers in Genetics·Bruno T L NichioRoberto Tadeu Raittz
Feb 8, 2019·Applied Microbiology and Biotechnology·Mariano A Torres MannoMartín Espariz

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Software Mentioned

phylip
OF
CentOS
Gclust
Ortholog
OM
Finder
InParanoid
indel
Basic Local Alignment Search Tool ( BLAST )

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