ksrates

ksrates analyzes whole-genome duplication (WGD) events relative to speciation by using substitution-rate-adjusted mixed paralog–ortholog Ks distributions to position ancient WGDs within phylogenetic contexts.

Key Features:

• Substitution-rate adjustment: Adjusts for lineage-specific differences in substitution rates to enable accurate comparison of Ks distributions.
• Mixed paralog–ortholog Ks distributions: Leverages combined paralog and ortholog Ks distributions to relate duplication peaks to speciation events.
• Paralog and ortholog Ks analysis: Analyzes paralog (within-genome duplicates) and ortholog (between-species) Ks values.
• Input sequence types: Processes Ks distributions derived from genomic and transcriptomic sequences.
• Implementation: Implemented in Python 3.
• Phylogenetic positioning of WGDs: Positions ancient WGD occurrences relative to speciation within phylogenetic frameworks.

Scientific Applications:

• Phylogenetic analysis: Positions WGD events relative to speciation to inform evolutionary history and timing of genomic changes.
• Comparative genomics: Compares Ks distributions across species or lineages to elucidate patterns of genome evolution.

Methodology:

Analyzes paralog and ortholog Ks values and applies lineage-specific substitution-rate adjustments to determine the timing of WGD events relative to speciation.