Welcome to BEASTling’s documentation!

A linguistics-focussed command line tool for easily generating BEAST 2.x XML files for phylogenetic analyses.

Contents

• Overview
  • Motivation
  • What does BEASTling actually do?
• Installation
  • Dependencies
  • Installation methods
• Tutorial
  • Fundamentals
  • Installation
  • Using BEASTling
  • More advanced modelling
  • Best practices
• Usage
  • Basic usage
  • Running your analysis
  • Sampling from the prior
  • Verbose mode
  • Generating reports
  • Generating language lists
  • Extracting configurations from XMLs
  • Advanced stuff
• Configuration file
  • admin section
  • MCMC section
  • languages section
  • model sections
  • clock sections
  • geography section
  • geo_priors section
• Data formats
  • BEASTling format
  • CLDF format
• Modelling details
  • Tree prior
  • Branch lengths
  • Clocks
• Clock models
  • Strict
  • Uncorrelated Relaxed Clock
  • Random Local Clock
• Substitution models
  • Binary CTMC
  • Binary Covarion
  • Mk
  • BSVS
• Advanced features
  • Ancestral state reconstruction
  • Path sampling
• Scripting BEASTling
  • Example
  • Creating Configurations from scratch