molpopgen
Faculty member in Ecology & Evolutionary Biology at UC Irvine. @ThorntonLab is our group's GitHub account.
University of California IrvineIrvine, CA
Pinned Repositories
BigDataFormats
Tutorial on programming or "big data"/bioinformatics
fwdpp
fwdpp is a C++ template library for implementing efficient forward-time population genetic simulations
fwdpy
forward-time population genetic simulation in python
fwdpy11
Forward-time simulation in Python using fwdpp
gimp_scripts
Plugins for GIMP
libsequence
libsequence: a C++ class library for evolutionary genetic analysis
msstats
msstats calculates many common popgen summary statistics from the output of the coalescent simulation "ms".
pecnv
C++ tools for calling structural variants from PE mapping of short reads.
molpopgen's Repositories
molpopgen/libsequence
libsequence: a C++ class library for evolutionary genetic analysis
molpopgen/BigDataFormats
Tutorial on programming or "big data"/bioinformatics
molpopgen/gimp_scripts
Plugins for GIMP
molpopgen/fwdpy
forward-time population genetic simulation in python
molpopgen/msstats
msstats calculates many common popgen summary statistics from the output of the coalescent simulation "ms".
molpopgen/pylibseq
Python interface to libsequence via pybind11
molpopgen/md2Canvas
Examples of canvas questions written in Markdown
molpopgen/fwdpy11_arg_example
Example of tracking the ARG during forward simulations. Implementation is a Python package using fwdpp, fwdpy11, msprime, and pybind11.
molpopgen/sweepsims
A collection of coalescent simulations of selective sweeps written over the years. (See wiki for citation info, please.)
molpopgen/bioconda-recipes
Conda recipes for the bioconda channel.
molpopgen/dummy
Crash test dummy repo for this numpy/msprime issue.
molpopgen/example_tskit_rust_simulations
Examples of forward-time simulations written using tskit-rust
molpopgen/fdr_perm
molpopgen/FixedCrossoverInterval
Example of extending fwdpy11 to add a new GeneticMapUnit type
molpopgen/fwdpp_tsms
molpopgen/fwdpy11_frequency_tracker
molpopgen/md_test
mardown to pdf via pandoc + latex
molpopgen/new_fake_repo
molpopgen/online_teaching_notes
Technical notes to self re: moving courses online
molpopgen/polytable2
Refactoring libsequences PolyTable is a big deal, so we're doing it outside of the library first.
molpopgen/qtrait_paper
Scripts, etc., for polygenic adaptation paper
molpopgen/remark_testing
molpopgen/rnarkdown_notes_example
molpopgen/TennessenEAonly
The EA demographic model from Tennessen et al.
molpopgen/tikz_graphics
Repository of tikz graphics. Mostly for testing/self education.
molpopgen/tree_representation
Examples of tree representation and performance.
molpopgen/tskit-paper
molpopgen/tskit-site
tskit website
molpopgen/tskit_tutorial_mockups
tskit tutorials written in R markdown
molpopgen/ViennaTalk2019
Talk given at polygenic adaptation meeting