Software from the Thornton lab
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:
- 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
- forrustts refines ideas that began with fwdpp and will eventually completely replace that project.
C++ software libraries
The following tools are no longer maintained and are unsupported. Most have been superceded by better tools, either by us or by others.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 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