mrpast Overview
mrpast is a tool for inferring demographic parameters from phased genomic data. It uses Ancestral Recombination Graphs (for an overview of ARGs, see here). You can either infer ARGs from your data yourself, or use one of mrpast’s integrations with Relate, tsinfer, or SINGER.
Usage Modes
mrpast takes a user-specified model as input. We have a bunch of
example models
that are a good starting place, and you can look at the modeling section of the docs as well.
Models specify a ground_truth value for each parameter, which can be set to a random value initially (if you
don’t know an expected value). The upside of providing a ground_truth value is that you can then simulate the
input model.
Simulating input models lets you explore the identifiability of the model with respect to mrpast. You can simulate
ARGs from a model, and if mrpast cannot accurately identify the model parameters then it is unlikely to be a useful
model on real data. Once you have verified that the simulated ARGs can be useful for mrpast, you can convert
the simulated ARGs to raw data (mrpast sim2vcf) and then re-infer ARGs (mrpast arginfer) to see if the
results are still accurate on inferred ARGs.
If a model behaves well with both simulated ARGs and inferred ARGs on simulated data, then you can move on to real data.
Simplest Usage Example
Below is the simplest usage for mrpast, which generates and processes simulated ARGs with a constant recombination rate. This example only takes a couple minutes to run end-to-end on a typical laptop.
# Install
pip install mrpast
# Download one of the example models
wget https://github.com/aprilweilab/mrpast/raw/refs/heads/main/examples/5deme1epoch.yaml
# Simulate some ARGs
mkdir -p 5d1e.simdata && mrpast simulate -j 6 5deme1epoch.yaml 5d1e.simdata/5d1e_
# Process the coalescence distribution from the ARGs and solve the maximum likelihood parameters
mkdir -p 5d1e.output && mrpast process -j 6 --solve --out-dir 5d1e.output/ --bootstrap coalcounts 5deme1epoch.yaml 5d1e.simdata/5d1e_
The last command above will emit a message like “The output with the highest likelihood is 5d1e.output/5deme1epoch.bfc276c6.solve_in.bootstrap.3.out.json” at the end. We can then use the “mrpast show” command to see the results from that output:
# Show the parameter values for the best result
mrpast show 5d1e.output/5deme1epoch.bfc276c6.solve_in.bootstrap.3.out.json
Further Information
Use the links below or on the left menu-bar to learn more.