ksrates: positioning whole-genome duplications relative to speciation events in KS distributions

Cecilia Sensalari; Steven Maere; Rolf Lohaus

doi:10.1093/bioinformatics/btab602

ksrates: positioning whole-genome duplications relative to speciation events in KS distributions

Bioinformatics. 2022 Jan 3;38(2):530-532. doi: 10.1093/bioinformatics/btab602.

Authors

Cecilia Sensalari^{1

2}, Steven Maere^{1

2}, Rolf Lohaus^{1

2}

Affiliations

¹ Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent 9052, Belgium.
² VIB Center for Plant Systems Biology, Ghent 9052, Belgium.

PMID: 34406368
DOI: 10.1093/bioinformatics/btab602

Abstract

Summary: We present ksrates, a user-friendly command-line tool to position ancient whole-genome duplication events with respect to speciation events in a phylogeny by comparing paralog and ortholog KS distributions derived from genomic or transcriptomic sequences, while adjusting for substitution rate differences among the lineages involved.

Availability and implementation: ksrates is implemented in Python 3 and as a Nextflow pipeline. The source code, Singularity and Docker containers, documentation and tutorial are available via https://github.com/VIB-PSB/ksrates.

Supplementary information: Supplementary data are available at Bioinformatics online.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Gene Duplication*
Genome*
Genomics
Phylogeny
Software

Grants and funding

VIB and Ghent University