Welcome to ksrates documentation!

• K_S rate-adjustment
  • Substitution rate-adjustment strategy in a nutshell
  • Explained example
• Installation
  • Nextflow (recommended)
  • Apptainer and Docker containers
  • Manual installation
  • Testing your installation
  • Updating your installation
• Usage
  • Run example case as a Nextflow pipeline (recommended)
  • Run example case as a manual pipeline
  • Practical considerations
• Input and output description
  • Input files
  • Output files and directory organization
  • Note on wgd output files
• Configuration files
  • ksrates configuration file
  • Nextflow configuration file
  • Expert configuration file
• Mixture modeling of paralog K_S distributions
  • Anchor K_S clustering
  • Exponential-lognormal mixture model
  • Lognormal mixture model
• Reciprocally retained gene families for plant WGMs
  • Concept
  • Reciprocal retention pipeline
  • Runtime, memory and space usage
  • Note on OrthoMCL implementation
  • Feedback
• FAQs about ksrates
  • Nextflow
  • Containers
  • General errors and warnings
  • Configuration
• How to cite us