<i>ksrates</i> : positioning whole-genome duplications relative to speciation events in <i>K</i> S distributions
Cecilia Sensalari, Steven Maere, Rolf Lohaus
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.
Topics & Concepts
Python (programming language)DocumentationSource codeGenomeGene duplicationBiologyComputer scienceGenetic algorithmComputational biologyEvolutionary biologyGeneticsProgramming languageGeneGenomics and Phylogenetic StudiesChromosomal and Genetic VariationsGenome Rearrangement Algorithms