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

BEASTling

Navigation

  • Overview
  • Installation
  • Tutorial
  • Usage
  • Configuration file
  • Data formats
  • Modelling details
  • Clock models
  • Substitution models
  • Advanced features
  • Scripting BEASTling

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