silastittes

shiny_popgen

Shiny apps for teaching Population Genetics

cds_fold

Outputs the 0-fold and 4-fold sites from a gff and reference genome.

performr

rdmc

R package implementing convergent adaptation models of Lee and Coop (2017)

tidy_vcf

Converts a sample of sites from standard VCF table into tidy format for easy summary stats and plotting.

gpfreqs

random_seqmask

Input a fasta of sequence, masks each sequence randomly according to input parameters. Allows identical masking across the input sequences or random masking.

abc-nam

abc_maize

analysis2

Analysis for the second consortium paper.

analysis2_manuscript

manuscript repo for the paper describing selection additions and analysis

cv

My Curriculum vitae

degenotate

DFE-alpha_CLI

A wrapper for running the DFE-alpha software

diploSHIC

dna-seq-gatk-variant-calling

locator

deep learning prediction of geographic location from individual genome sequences

ms_sub

msmc2_to_usfs

panand_structure

Simple nextflow pipeline for running NGSadmix starting with a VCF

parv_local

penta_channel

pyslim

Tools for dealing with tree sequences coming to and from SLiM.

ReLERNN

Recombination Landscape Estimation using Recurrent Neural Networks

SLiM

SLiM is a genetically explicit forward simulation software package for population genetics and evolutionary biology. It is highly flexible, with a built-in scripting language, and has a cross-platform graphical modeling environment called SLiMgui.

slim_bgs

Simple SLiM code to think about background selection and sweeps.

stdpopsim

A library of standard population genetic models

summarize_bams

Little script to produce data about sites from a list of bam files.

sweep_regions

command line tool to define outliers and merge them into regions

tribolium_pipeline