population-genetics
There are 12 repositories under population-genetics topic.
- anvioLanguage:Python 485
projectglow / glow
An open-source toolkit for large-scale genomic analysis
Language:Scala 287- Language:R 262
- Language:Nextflow 178
- Language:C 164
- pophelper
royfrancis / pophelper
An R package to analyse and visualise admixture proportions from STRUCTURE, fastSTRUCTURE, TESS, ADMIXTURE etc.
Language:R 148 - SNPGenie
chasewnelson / SNPGenie
Program for estimating πN/πS, dN/dS, and other diversity measures from next-generation sequencing data
Language:Perl 117 starskyzheng / panpop
Application of pan-genome for population
Language:Perl 104- Language:Python 100
- grenepipe
moiexpositoalonsolab / grenepipe
A flexible, scalable, and reproducible pipeline to automate variant calling from raw sequence reads, with lots of bells and whistles - for sampled individuals, and for pool sequencing.
Language:Python 96 BGI-shenzhen / VCF2Dis
VCF2Dis: A new simple and efficient software to calculate p-distance matrix and construct population phylogeny based Variant Call Format
Language:C++ 84AI-sandbox / neural-admixture
Rapid population clustering with autoencoders
Language:Python 73- Language:C 72
- poppr
grunwaldlab / poppr
🌶 An R package for genetic analysis of populations with mixed (clonal/sexual) reproduction
Language:R 70 - Language:C++ 64
vinuesa / get_phylomarkers
A pipeline to select optimal markers for microbial phylogenomics and species tree estimation using the multispecies coalescent and concatenation approaches
Language:Perl 59- Language:R 58
- Language:R 56
- Language:Python 54
- Language:Python 49
- Language:C++ 44
mklarqvist / tomahawk
Fast calculations of linkage-disequilibrium in large-scale human cohorts
Language:C++ 43- grenedalf
lczech / grenedalf
Toolkit for Population Genetic Statistics from Pool-Sequenced Samples, e.g., in Evolve and Resequence experiments
Language:C++ 40 gtonkinhill / rhierbaps
rhierbaps: R implementation of hierBAPS
Language:R 35- Language:Python 34
aprilweilab / grgl
Genotype Representation Graph Library
Language:C++ 33- Language:R 33
- Language:C++ 30
EricArcher / strataG
strataG is a toolkit for haploid sequence and multilocus genetic data summaries, and analyses of population structure.
Language:HTML 26- Language:HTML 25
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.
Language:Python 22Zilong-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.
Language:C++ 22- Language:Python 20
SchriderLab / Timesweeper
Python package for detecting positive selective sweeps using time-series genomics sampling data.
Language:Python 20stephenturner / kgp
1000 Genomes Project Metadata R Package
Language:R 20sanjaynagi / rna-seq-pop
Snakemake workflow for Illumina RNA-sequencing experiments - extract population genomic signals from RNA-Seq data
Language:Jupyter Notebook 18
