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analysis2

Analysis for the second consortium paper.

angsd

Program for analysing NGS data.

arg-dating-debug

arg-dating-paper

Variational dating of ancestral recombination graphs

coaldecoder

Demographic inference from trio coalescence rates

cormlpe

a corStruct class for nlme, implementation of Clarke's maximum likelihood population effects model

cormlpe_unsupported

eigentest

epee

scalable expectation-propagation for the phylogenetic threshold model

epee2

scalable expectation-propagation for the phylogenetic threshold model

eucpru-popsim-data

Auxiliary data for Eucera pruinosa genomic simulations from Pope et al

hdngsd

tools for analysis of sequence data from mixed haplo-diploid samples

hiscott2d

Likelihood calculation for two-trait phylogenetic threshold model

inlassle

locator

deep learning prediction of geographic location from individual genome sequences

msprime

A reimplementation of Hudson's classical ms simulator for modern data sets.

ngsparalog

Copy number variation detection using NGS data.

paternitydp

popbio

a short graduate population biology course

product-space-fem

r2vcftools

radish

Fast gradient-based optimization of resistance surfaces

radish-manuscript

radishdgs

simulation for radish DGS project

relate

Software for estimating genome-wide genealogies for thousands of samples

relate_lib

C++ library containing functions for parsing/dumping Relate output files

rphylopars

Phylogenetic Comparative Tools for Missing Data and Within-Species Variation

sibship-foraging

Sibship foraging models using resistance distance

singer-snakemake

Snakemake workflow for SINGER (ARG sampling)

slim_magic

ipython magic for simulation using SLiM