Tree2GD: a phylogenomic method to detect large-scale gene duplication events

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Abstract
Whole-genome duplication events have long been discovered throughout the evolution of eukaryotes, contributing to genome complexity and biodiversity and leaving traces in the descending organisms. Therefore, an accurate and rapid phylogenomic method is needed to identify the retained duplicated genes on various lineages across the target taxonomy. Here, we present Tree2GD, an integrated method to identify large-scale gene duplication events by automatically perform multiple procedures, including sequence alignment, recognition of homolog, gene tree/species tree reconciliation, Ks distribution of gene duplicates and synteny analyses. Application of Tree2GD on 2 datasets, 12 metazoan genomes and 68 angiosperms, successfully identifies all reported whole-genome duplication events exhibited by these species, showing effectiveness and efficiency of Tree2GD on phylogenomic analyses of large-scale gene duplications. Tree2GD is written in Python and C++ and is available at https://github.com/Dee-chen/Tree2gd Supplementary data are available at Bioinformatics online.
Funding Information
  • National Natural Science Foundation of China (32070247)
  • China Postdoctoral Science Foundation (2019M661344)
  • State Key Laboratory of Genetic Engineering and Ministry of Education Key Laboratory of Biodiversity Science and Ecological Engineering in Fudan University

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