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

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 substit...

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Bibliographic Details
Published in:Bioinformatics 2022-01, Vol.38 (2), p.530-532
Main Authors: Sensalari, Cecilia, Maere, Steven, Lohaus, Rolf
Format: Article
Language:English
Subjects:
Gene Duplication
Genome
Genomics
Phylogeny
Software
Online Access:Request full text
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Description
Summary: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.
ISSN:1367-4803
1460-2059
1367-4811
DOI:10.1093/bioinformatics/btab602