Jared G. Galloway, M.Sc.
Bridger Mountains, Montana
ReLERNN - Recombination Landscape Estimation using Recurrent Neural Networks. ReLERNN uses deep learning to infer the genome-wide landscape of recombination from as few as four samples. This repository contains the code and instructions required to run ReLERNN, and includes example files to ensure everything is working properly. The current manuscript detailing ReLERNN can be found here.
This is the code for endcoding a
tskitTreeSequence Object into a 3D array for ML and visualization purposes.
stdpopsim -A community-maintained library of standard simulation population genetic simulation models. Please see the documentation for further details.
tskit - Succinct tree sequences are a highly efficient way of storing a set of related DNA sequences by storing their ancestral history as a set of correlated trees along the genome. The tree sequence format is output by a number of software libraries and programs (such as msprime, SLiM, fwdpp, and tsinfer) that either simulate or infer the evolutionary history of genetic sequences. The
tskitlibrary provides the underlying functionality used to load, examine, and manipulate tree sequences. It often forms part of an installation of other software packages such as those listed above. Please see the documentation for further details, which includes installation instructions.
SLiM - SLiM is an evolutionary simulation framework that combines a powerful engine for population genetic simulations with the capability of modeling arbitrarily complex evolutionary scenarios. Simulations are configured via the integrated Eidos scripting language that allows interactive control over practically every aspect of the simulated evolutionary scenarios. The underlying individual-based simulation engine is highly optimized to enable modeling of entire chromosomes in large populations.
Analysis pipeline (stdpopsim) - This directory contains the code to run analysis of demographic inferance using multiple programs, with identical resulting data from any demographic model found in
stdpopsimas input to each. This provides an example of how standardized population simulations may be used to compare methods. The Snakemake workflow includes the neccesary pipeline for simulation, analyses, and plotting in an effecient manner. Simply choose your parameters in a config file, and let snakemake handle the rest.
Squirrel Suiter - Squirrel Suiter is an endless “flyer” game where you play as a jetpack-equipped flying squirrel, avoiding obstacles and munching acorns to gain the highest score. This can be played on any google play equipped device.