Implementation of the multiple sequential markovian coalescent
☆91Aug 5, 2025Updated 7 months ago
Alternatives and similar repositories for msmc
Users that are interested in msmc are comparing it to the libraries listed below
Sorting:
- ☆68Dec 5, 2022Updated 3 years ago
- Tools and Utilities for msmc and msmc2☆50Jan 23, 2026Updated last month
- Implementation of the Pairwise Sequentially Markovian Coalescent (PSMC) model☆185Nov 17, 2025Updated 4 months ago
- SMC++ infers population history from whole-genome sequence data.☆173Jan 20, 2024Updated 2 years ago
- MSMC2 Scripts☆28Sep 24, 2025Updated 5 months ago
- Program for analysing NGS data.☆256Mar 6, 2025Updated last year
- 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
- Infer demographic history with the Moran model☆51Jun 14, 2025Updated 9 months ago
- RRSelection: A linkage disequilibrium method to detect selection region across population VCF☆14Feb 11, 2019Updated 7 years ago
- Fast calculation of Patterson's D (ABBA-BABA) and the f4-ratio statistics across many populations/species☆186Dec 19, 2024Updated last year
- Sampling and manipulating genome-wide ancestral recombination graphs (ARGs)☆14May 1, 2023Updated 2 years ago
- ☆21Jan 11, 2024Updated 2 years ago
- Codes for Vmap1.1 and Vmap3☆11Jan 5, 2026Updated 2 months ago
- Simple pipeline to go from an alignment to a neutral model, using the PHAST toolkit☆11Jan 17, 2020Updated 6 years ago
- predicting DFE and alpha from polymorphism data☆28Oct 4, 2018Updated 7 years ago
- General tools for genomic analyses.☆387Feb 28, 2025Updated last year
- Analysis of inference methods on standard population models☆25Dec 3, 2021Updated 4 years ago
- 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
- Effective selection of population size projection for construction of the site frequency spectrum. Convert VCF to dadi/fastsimcoal style …☆172Aug 8, 2024Updated last year
- Tutorial on using popular tools for learning about population history☆53Jul 18, 2018Updated 7 years ago
- cobraa (coalescent based reconstruction of ancient admixture): a hidden Markov model to infer ghost admixture using just a diploid sequen…☆23Jun 17, 2025Updated 9 months ago
- HaploSweep is a method for detecting and categorizing soft and hard selective sweeps based on haplotype structure.☆11Sep 24, 2024Updated last year
- Genome-wide scan for balancing selection using beta statistic☆32Apr 26, 2023Updated 2 years ago
- Topology weighting by iterative sampling of sub-trees☆86Jan 5, 2025Updated last year
- Software for estimating genome-wide genealogies for thousands of samples☆41Oct 17, 2025Updated 5 months ago
- Estimating Effective Migration Surfaces☆111Oct 28, 2023Updated 2 years ago
- Framework for analyzing low depth NGS data in heterogeneous populations using PCA.☆60Jun 27, 2025Updated 8 months ago
- use long sequenced reads to close gaps in assemblies☆41Sep 4, 2018Updated 7 years ago
- Two locus likelihoods and ARGs under changing population size☆14Dec 18, 2025Updated 3 months ago
- Haplotype based scans for selection☆142Mar 10, 2026Updated last week
- A tool for estimating time-dependent migration rates based on cross-/within-population coalescent rates from MSMC☆16Apr 6, 2025Updated 11 months ago
- Scripts to analyze data using TreeMix. This pipeline runs TreeMix with bootstrapping, helps choose number of migration events and creates…☆46Mar 7, 2024Updated 2 years ago
- machine learning applications for dadi☆17Jan 23, 2025Updated last year
- PopLDdecay: a fast and effective tool for linkage disequilibrium decay analysis based on variant call format(VCF) files☆203Aug 15, 2024Updated last year
- Topology weighting from unphased genotypes of any ploidy☆23Updated this week
- Tutorials on phylogenetic and phylogenomic inference☆395Sep 13, 2023Updated 2 years ago
- LDBlockShow: a fast and convenient tool for visualizing linkage disequilibrium and haplotype blocks based on VCF files☆36Jul 5, 2025Updated 8 months ago
- Time-stratified f-statistics☆15Aug 1, 2025Updated 7 months ago
- A Shiny-based server framework for retrieving, analyzing and visualizing the large genomic variations data in a lab.☆20Oct 28, 2024Updated last year