population-genetics
There are 278 repositories under population-genetics topic.
merenlab/anvio
An analysis and visualization platform for 'omics data
projectglow/glow
An open-source toolkit for large-scale genomic analysis
knausb/vcfR
Tools to work with variant call format files
lh3/psmc
Implementation of the Pairwise Sequentially Markovian Coalescent (PSMC) model
nf-core/eager
A fully reproducible and state-of-the-art ancient DNA analysis pipeline
royfrancis/pophelper
An R package to analyse and visualise admixture proportions from STRUCTURE, fastSTRUCTURE, TESS, ADMIXTURE etc.
chasewnelson/SNPGenie
Program for estimating πN/πS, dN/dS, and other diversity measures from next-generation sequencing data
starskyzheng/panpop
Application of pan-genome for population
moiexpositoalonsolab/grenepipe
A flexible, scalable, and reproducible pipeline to automate variant calling from raw sequence reads, with lots of bells and whistles.
bacpop/PopPUNK
PopPUNK 👨🎤 (POPulation Partitioning Using Nucleotide Kmers)
BGI-shenzhen/VCF2Dis
VCF2Dis: A new simple and efficient software to calculate p-distance matrix and construct population phylogeny based Variant Call Format
grunwaldlab/poppr
🌶 An R package for genetic analysis of populations with mixed (clonal/sexual) reproduction
AI-sandbox/neural-admixture
Rapid population clustering with autoencoders
precimed/mixer
Causal Mixture Model for GWAS summary statistics
lczech/genesis
A library for working with phylogenetic and population genetic data.
CBIIT/LDlinkR
LDlinkR
bodkan/slendr
Population genetic simulations in R 🌍
vinuesa/get_phylomarkers
A pipeline to select optimal markers for microbial phylogenomics and species tree estimation using the multispecies coalescent and concatenation approaches
kr-colab/diploSHIC
feature-based deep learning for the identification of selective sweeps
kr-colab/locator
deep learning prediction of geographic location from individual genome sequences
mklarqvist/tomahawk
Fast calculations of linkage-disequilibrium in large-scale human cohorts
Zilong-Li/PCAone
Fast, Accurate and Memory-Efficient Principal Component Analysis All in One
lczech/grenedalf
Toolkit for Population Genetic Statistics from Pool-Sequenced Samples, e.g., in Evolve and Resequence experiments
gtonkinhill/rhierbaps
rhierbaps: R implementation of hierBAPS
alek0991/iSAFE
Pinpoints the mutation favored by selection
molpopgen/fwdpy11
Forward-time simulation in Python using fwdpp
bodkan/admixr
An R package for reproducible and automated ADMIXTOOLS analyses
EricArcher/strataG
strataG is a toolkit for haploid sequence and multilocus genetic data summaries, and analyses of population structure.
jgx65/hierfstat
the hierfstat package
Zilong-Li/vcfpp
a C++ API of htslib to be easily integrated and safely used. More importantly, it can be callled seamlessly in R/Python/Julia etc.
aprilweilab/grgl
Genotype Representation Graph Library
CBIIT/nci-webtools-dceg-linkage
LDlink is a suite of web-based applications designed to easily and efficiently interrogate linkage disequilibrium in population groups. Each included application is specialized for querying and displaying unique aspects of linkage disequilibrium.
stephenturner/kgp
1000 Genomes Project Metadata R Package
fengcong3/HAPPE
A tool to visualize the haplotype pattern and various information in excel.
sanjaynagi/rna-seq-pop
Snakemake workflow for Illumina RNA-sequencing experiments - extract population genomic signals from RNA-Seq data
SchriderLab/Timesweeper
Python package for detecting positive selective sweeps using time-series genomics sampling data.