Framework for analyzing low depth NGS data in heterogeneous populations using PCA.
☆62Jun 27, 2025Updated last year
Alternatives and similar repositories for pcangsd
Users that are interested in pcangsd are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- Site frequency spectrum estimation based on window expectation-maximisation algorithm☆17May 19, 2023Updated 3 years ago
- EM-PCA for Ultra-low Coverage Sequencing Data☆20Dec 18, 2025Updated 9 months ago
- Program for analysing NGS data.☆268Mar 6, 2025Updated last year
- Pipeline for GTseq genotyping and quality control☆17Jan 30, 2023Updated 3 years ago
- WinPCA. A package for windowed principal component analysis.☆54Jun 9, 2026Updated 4 months ago
- Deploy to Railway using AI coding agents - Free Credits Offer • AdUse Claude Code, Codex, OpenCode, and more. Autonomous software development now has the infrastructure to match with Railway.
- SNP genotyping in polyploids☆17Aug 12, 2020Updated 6 years ago
- Haplotype and population structure inference using neural networks.☆30Dec 5, 2024Updated last year
- Fast calculation of Patterson's D (ABBA-BABA) and the f4-ratio statistics across many populations/species☆192Dec 19, 2024Updated last year
- loco-pipe is an automated Snakemake pipeline that streamlines a set of essential population genomic analyses for low-coverage whole genom…☆37Jan 21, 2026Updated 8 months ago
- Calculation of pairwise Linkage Disequilibrium (LD) under a probabilistic framework☆53Nov 13, 2023Updated 2 years ago
- Lift-over alignments from variant-aware references☆34Mar 4, 2023Updated 3 years ago
- mixture classification, constraint optimization, outlier detection, population structure, admixture history, and selection detection.☆90Jun 14, 2021Updated 5 years ago
- R Package to Estimate Variable Recombination Rates using Population Genetic Data☆45Nov 13, 2019Updated 6 years ago
- Software for ancestry estimation in unrelated individuals☆26Jan 31, 2026Updated 8 months ago
- Managed hosting for WordPress and PHP on Cloudways • AdManaged hosting for WordPress, Magento, Laravel, or PHP apps, on multiple cloud providers. Deploy in minutes on Cloudways by DigitalOcean.
- ☆50Jun 26, 2026Updated 3 months ago
- Estimation of per-individual inbreeding tracts under a probabilistic framework☆16Aug 11, 2023Updated 3 years ago
- Pipelines for analyzing genomic or transcriptomic data☆17Feb 29, 2024Updated 2 years ago
- ☆112Oct 14, 2021Updated 4 years ago
- A statistical framework for reference-free inference of archaic local ancestry☆15Nov 8, 2019Updated 6 years ago
- Versatile tool for detecting selective sweeps with a variety of ages, strengths, starting allele frequencies, and completeness.☆15Feb 16, 2026Updated 7 months ago
- Recombination Landscape Estimation using Recurrent Neural Networks☆73Mar 27, 2026Updated 6 months ago
- QUILT: Low coverage whole genome sequence imputation with large reference panels☆68Updated this week
- linearize and simplify variation graphs using blocked partial order alignment☆67Aug 21, 2026Updated last month
- AI Agents on DigitalOcean Gradient AI Platform • AdBuild production-ready AI agents using customizable tools or access multiple LLMs through a single endpoint. Create custom knowledge bases or connect external data.
- GenMap - Fast and Exact Computation of Genome Mappability☆124Jun 20, 2024Updated 2 years ago
- Cool Bioinformatics Scripts☆12May 21, 2024Updated 2 years ago
- Genotype likelihood simulator for VCF/BCF files☆17May 7, 2025Updated last year
- Ancestry_HMM-S is program designed to infer adaptive introgression from population genomic data☆20Sep 25, 2023Updated 3 years ago
- Module for analysing admixture graphs☆30Apr 30, 2018Updated 8 years ago
- An R package to detect, classify, and visualize genome rearrangements☆15Aug 4, 2020Updated 6 years ago
- SMC++ infers population history from whole-genome sequence data.☆178Jan 20, 2024Updated 2 years ago
- Estimation of per-individual inbreeding coefficients under a probabilistic framework☆22Aug 8, 2023Updated 3 years ago
- A script to extract graph structure from multiple sequence alignment result and output as GFA/JSON for vg☆11Mar 27, 2019Updated 7 years ago
- Managed hosting for WordPress and PHP on Cloudways • AdManaged hosting for WordPress, Magento, Laravel, or PHP apps, on multiple cloud providers. Deploy in minutes on Cloudways by DigitalOcean.
- Genome-wide scan for balancing selection using beta statistic☆32Apr 26, 2023Updated 3 years ago
- ☆12Nov 23, 2020Updated 5 years ago
- Tree reconstruction of ancestry using incomplete lineage sorting☆11Jan 9, 2026Updated 9 months ago
- Methods for examining PCA locally along the genome.☆91Aug 13, 2024Updated 2 years ago
- a short graduate population biology course☆13Feb 22, 2023Updated 3 years ago
- Code to compute the XP-CLR statistic to infer natural selection☆108Jun 13, 2022Updated 4 years ago
- ☆29Jul 16, 2022Updated 4 years ago