Software from the Thornton lab

GitHub accounts

• Kevin Thornton
• Thornton Lab
• Forward Simulation
• tskit.dev

Software projects

The list below is mostly related to code resulting from publications. There is a lot of other code available from GitHub accounts associated with lab members:

Simulation software

• fwdpy11 is a powerful Python environment for forward-time simulation. It uses fwdpp as its back-end.

• pylibseq is a Python interface to libsequence that can be used to analyze output from msprime and fwdpy11.

• ABCreg is a tool for performing statistical inference via approximate Bayesian computation, or ABC. The software was first described here.

Rust crates

• tskit-rust is a rust interface to tskit. In addition to the API reference, there is also a book.
• demes-rs is a rust implementation of the demes standard. See here for more about demes.
• demes-forward-rs provides an API for forward-time traversal of demes graphs.
• demes-forward-capi defined a C API allowing C/C++/etc. access to demes-forward.
• forrustts refines ideas that began with fwdpp and will eventually completely replace that project.

C++ software libraries

• libsequence is a C++ software library for evolutionary genetic analysis. The citation for this work is a paper from 2003

• fwdpp is a C++ template library for developing forward-time simulations under population- and quantitative- genetic models. I published a description of the library in Genetics.

Retired software

The following tools are no longer maintained and are unsupported. Most have been superceded by better tools, either by us or by others. They are listed here because they have been used in papers, and so we keep the code available for archival purposes.

• Code for simulating a neutral coalescent process for copy-number variants that I used in Thornton 2007

• Code from Thornton and Jensen (2007). This code simulates a sweep in a bottlenecked population, plus the ancestral population. See paper for details.

• Code for models of recurrent hitch-hlking used in Jensen, Thornton and Andolfatto (2008) PLoS Genetics

• msstats processes the output of coalescent simulations and calculates various summary statistics

• omega Calculates Kim and Nielsen’s (2004, Genetics 167:1513) “omega_max” statistic which was explored in Jensen et al. (2007, Genetics 176 2371-3279). Please read the source code for documentation. Both Kim and Nielsen and Jensen et al. should be cited if this code is used—the first for the statistic, the latter for the implementation.

• msld calculates LD-related statistics from the output of simulations using the same format as Hudson’s ms.

• analysis programs for the (pre-NGS-era) analysis of population-genetic data.

• sequtils is a set of tools for manipulation of (pre-NGS-era) sequence data. (Probably only for old folks at this point in time…)

Written on: Nov 16 2022