population-genetics
There are 11 repositories under population-genetics topic.
- anvioLanguage:Python 402
projectglow / glow
An open-source toolkit for large-scale genomic analysis
Language:Scala 258- Language:R 233
- Language:C 141
- pophelper
royfrancis / pophelper
An R package to analyse and visualise admixture proportions from STRUCTURE, fastSTRUCTURE, TESS, ADMIXTURE etc.
Language:R 134 - Language:Nextflow 125
- SNPGenie
chasewnelson / SNPGenie
Program for estimating πN/πS, dN/dS, and other diversity measures from next-generation sequencing data
Language:Perl 98 - Language:Python 79
- grenepipe
moiexpositoalonsolab / grenepipe
A flexible, scalable, and reproducible pipeline to automate variant calling from sequence reads.
Language:Python 79 BGI-shenzhen / VCF2Dis
VCF2Dis: A new simple and efficient software to calculate p-distance matrix based Variant Call Format
Language:C++ 72- poppr
grunwaldlab / poppr
🌶 An R package for genetic analysis of populations with mixed (clonal/sexual) reproduction
Language:R 67 starskyzheng / panpop
Application of pan-genome for population
Language:Perl 64- Language:C++ 56
AI-sandbox / neural-admixture
Rapid population clustering with autoencoders
Language:Python 52- Language:R 52
- Language:R 50
- Language:Python 47
- Language:C 47
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 47- Language:Python 45
mklarqvist / tomahawk
Fast calculations of linkage-disequilibrium in large-scale human cohorts
Language:C++ 40gtonkinhill / rhierbaps
rhierbaps: R implementation of hierBAPS
Language:R 32- Language:Python 30
- Language:C++ 27
- Language:C++ 27
- Language:R 26
EricArcher / strataG
strataG is a toolkit for haploid sequence and multilocus genetic data summaries, and analyses of population structure.
Language:HTML 25- Language:HTML 23
- grenedalf
lczech / grenedalf
Toolkit for Population Genetic Statistics from Pool-Sequenced Samples, e.g., in Evolve and Resequence experiments
Language:C++ 22 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 20stephenturner / kgp
1000 Genomes Project Metadata R Package
Language:R 19Zilong-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++ 18- Language:Python 16
sanjaynagi / rna-seq-pop
Snakemake workflow for Illumina RNA-sequencing experiments - extract population genomic signals from RNA-Seq data
Language:Jupyter Notebook 16pblischak / polyploid-genotyping
SNP genotyping in polyploids
Language:C++ 15- Language:Perl 15
