wgd v2: a suite of tools to uncover and date ancient polyploidy and whole-genome duplication.

MOTIVATION:Major improvements in sequencing technologies and genome sequence assembly have led to a huge increase in the number of available genome sequences. In turn, these genome sequences form an invaluable source for evolutionary, ecological, and comparative studies. One kind of analysis that has become routine is the search for traces of ancient polyploidy, particularly for plant genomes, where whole-genome duplication (WGD) is rampant. RESULTS:Here, we present a major update of a previously developed tool wgd, namely wgd v2, to look for remnants of ancient polyploidy, or WGD. We implemented novel and improved previously developed tools to a) construct KS age distributions for the whole-paranome (collection of all duplicated genes in a genome), b) unravel intra- and inter- genomic collinearity resulting from WGDs, c) fit mixture models to age distributions of gene duplicates, d) correct substitution rate variation for phylogenetic placement of WGDs, and e) date ancient WGDs via phylogenetic dating of WGD-retained gene duplicates. The applicability and feasibility of wgd v2 for the identification and the relative and absolute dating of ancient WGDs is demonstrated using different plant genomes. AVAILABILITY:wgd v2 is open source and available at https://github.com/heche-psb/wgd. SUPPLEMENTARY INFORMATION:Supplementary data are available at Bioinformatics online.