Welcome to Rarecoal’s Documentation!¶
Rarecoal is a software to model the population history of large sets of genomic samples from different populations. The main tool is called rarecoal and is maintained in the rarecoal github repository. Additional tools to prepare data for usage in rarecoal are maintained in the rarecoal-tools github repository. The project has been first reported in our publication on a genetic analyses of ancient Anglo-Saxon genomes from England, and further developed as reported in a recent preprint. The mathematical derivations can be found in the main github repository in the doc
directory.
Note
This documentation is written for rarecoal version 1.5.0, and rarecoal-tools version 1.2.7.
Contents:
- Installation instructions
- Rarecoal
- Histogram files
- Scaled Units
- Multithreading
- Demographic models
- Ghost Branches
- Excluding singletons and private variants
- Branch Shortening
- Computing the probability of a particular mutation pattern (rarecoal prob)
- Computing the likelihood of a histogram data set given a model (rarecoal logl)
- Parameter estimation using likelihood maximization (rarecoal maxl)
- Parameter estimation using Markov Chain Monte Carlo (rarecoal mcmc)
- Adding a branch to a model (rarecoal find)
- Investigating model fits (rarecoal fitTable)
- Simulating a model (rarecoal simCommand)
- Effective Nr of Sites correction
- Rarecoal Tools