Tools and Utilities for msmc and msmc2
☆50Jan 23, 2026Updated last month
Alternatives and similar repositories for msmc-tools
Users that are interested in msmc-tools are comparing it to the libraries listed below
Sorting:
- ☆68Dec 5, 2022Updated 3 years ago
- SMC++ infers population history from whole-genome sequence data.☆173Jan 20, 2024Updated 2 years ago
- Implementation of the multiple sequential markovian coalescent☆91Aug 5, 2025Updated 7 months ago
- Infer demographic history with the Moran model☆51Jun 14, 2025Updated 9 months ago
- Likelihood-based Selective Sweep Detection☆41Oct 12, 2023Updated 2 years ago
- MSMC2 Scripts☆28Sep 24, 2025Updated 5 months ago
- Population genetic summary statistics☆40Sep 28, 2023Updated 2 years ago
- Efficient program for calculating Extended Haplotype Homozygosity (EHH) and Integrated Haplotype Score (iHS)☆45Oct 24, 2019Updated 6 years ago
- Fast calculation of Patterson's D (ABBA-BABA) and the f4-ratio statistics across many populations/species☆186Dec 19, 2024Updated last year
- Two locus likelihoods and ARGs under changing population size☆14Dec 18, 2025Updated 3 months ago
- Tutorials on evolutionary genomics☆46Mar 11, 2022Updated 4 years ago
- Haplotype based scans for selection☆142Mar 10, 2026Updated last week
- Program for analysing NGS data.☆256Mar 6, 2025Updated last year
- Estimate recombination rates from population genetic data☆71Jun 10, 2020Updated 5 years ago
- defiNETti is a program for performing Bayesian inference on exchangeable (or permutation-invariant) data via deep learning. In particula…☆20Apr 10, 2018Updated 7 years ago
- mixture classification, constraint optimization, outlier detection, population structure, admixture history, and selection detection.☆88Jun 14, 2021Updated 4 years ago
- Simple pipeline to go from an alignment to a neutral model, using the PHAST toolkit☆11Jan 17, 2020Updated 6 years ago
- feature-based deep learning for the identification of selective sweeps☆59Feb 7, 2026Updated last month
- Tutorial on using popular tools for learning about population history☆53Jul 18, 2018Updated 7 years ago
- Heuristic, parsimony-based ancestral recombination graph inference☆17Aug 25, 2021Updated 4 years ago
- A tool for estimating time-dependent migration rates based on cross-/within-population coalescent rates from MSMC☆16Apr 6, 2025Updated 11 months ago
- ☆13Sep 11, 2025Updated 6 months ago
- Code to compute the XP-CLR statistic to infer natural selection☆103Jun 13, 2022Updated 3 years ago
- This is a read-only mirror of the CRAN R package repository. PopGenome — An Efficient Swiss Army Knife for Population Genomic Analyses …☆16Feb 3, 2020Updated 6 years ago
- RAiSD: software to detect positive selection based on multiple signatures of a selective sweep and SNP vectors☆40Nov 15, 2023Updated 2 years ago
- Tools for dealing with tree sequences coming to and from SLiM.☆28Mar 9, 2026Updated last week
- Implementation of the Pairwise Sequentially Markovian Coalescent (PSMC) model☆185Nov 17, 2025Updated 4 months ago
- ☆10Jan 18, 2023Updated 3 years ago
- An R package to estimate the timing of selection for a beneficial allele.☆14Dec 2, 2021Updated 4 years ago
- Tools for F1 hybrid PSMC (hPSMC) divergence time inference from whole genomes☆14May 29, 2024Updated last year
- A python framework for inferring demography from tracts of identity by state as reported in PLoS Genetics by Harris and Nielsen (2013)☆15Aug 1, 2013Updated 12 years ago
- The stairway plot is a method for inferring detailed population demographic history using the site frequency spectrum (SFS) from DNA sequ…☆65Sep 19, 2025Updated 6 months ago
- Minimal Assumption Genomic Inference of Coalescence☆14Aug 8, 2023Updated 2 years ago
- ABLE - Approximate Blockwise Likelihood Estimation☆17Jul 4, 2018Updated 7 years ago
- Coalescent Likelihood Under Effects of Selection - Inferring selection & allele frequency trajectories from nucleotide data☆26Jul 8, 2022Updated 3 years ago
- General tools for genomic analyses.☆387Feb 28, 2025Updated last year
- G-PhoCS is a software package for inferring ancestral population sizes, population divergence times, and migration rates from individual …☆34Apr 27, 2021Updated 4 years ago
- command-line tools for the management of genotype likelihoods and allele counts☆30Feb 12, 2024Updated 2 years ago
- Simulation of Epistasis Local adaptation, with Ancestry and Mate choice☆11Apr 22, 2023Updated 2 years ago