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Published on: March 22, 2018
Tree2GD: a phylogenomic method to detect large-scale gene duplication events
Duoyuan Chen1, Taikui Zhang1,2, Yamao Chen1
1State Key Laboratory of Genetic Engineering, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai 200433, China.
Motivation:
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.
Results:
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.
Availability And Implementation:
Tree2GD is written in Python and C++ and is available at https://github.com/Dee-chen/Tree2gd.
Supplementary Information:
Supplementary data are available at Bioinformatics online.
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