Programs from the popgen.dk group. Most now live on GitHub; the old wiki pages redirect there.
| ANGSD | Analysis of next generation sequencing data |
| NGSadmix | Admixture proportions from low depth NGS data |
| fastNGSadmix | Admixture proportions and PCA for a single NGS sample |
| PCAngsd | PCA, admixture and more for low depth NGS data |
| EMU | PCA with missing data |
| HaploNet | Haplotype clustering with neural networks |
| evalAdmix | Evaluate the fit of admixture results |
| asaMap | Ancestry-specific association mapping |
| NgsRelate | Relatedness and inbreeding from NGS data |
| IBSrelate | Relatedness from IBS patterns without allele frequencies |
| Relate | IBD sharing along the genome |
| RelateAdmix | Relatedness between admixed individuals |
| BAMSE | Bayesian association with multiple SNPs and environment |
| CATS | Power of two-stage association designs |
| refFinder | Extract bases from a fasta file |
| PCA and Fst in R | Eigenstrat-style PCA and Weir & Cockerham Fst |
Old download files are still at /software/download/.