cobraa (coalescent based reconstruction of ancient admixture): a hidden Markov model to infer ghost admixture using just a diploid sequence.
☆23Jun 17, 2025Updated 8 months ago
Alternatives and similar repositories for cobraa
Users that are interested in cobraa are comparing it to the libraries listed below
Sorting:
- machine learning applications for dadi☆17Jan 23, 2025Updated last year
- The GitHub for CLUES2, a method for inferring and evaluating evidence for selection.☆18Apr 9, 2025Updated 11 months ago
- Software for estimating genome-wide genealogies for thousands of samples☆40Oct 17, 2025Updated 4 months ago
- ☆12Sep 14, 2025Updated 5 months ago
- phyloGAN is a Generative Adversarial Network (GAN) that infers phylognetic relationships.☆11Jul 8, 2024Updated last year
- Statistical inference of recent positive selection using IBD segments☆14Sep 23, 2025Updated 5 months ago
- (Greetings_here_is_yet_another) Rate of Adaptive Protein Evolution Software☆10Jul 19, 2024Updated last year
- Sampling and manipulating genome-wide ancestral recombination graphs (ARGs)☆14May 1, 2023Updated 2 years ago
- HaploSweep is a method for detecting and categorizing soft and hard selective sweeps based on haplotype structure.☆11Sep 24, 2024Updated last year
- predicting DFE and alpha from polymorphism data☆28Oct 4, 2018Updated 7 years ago
- ☆17Nov 19, 2021Updated 4 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
- R Port of psmc☆17Mar 16, 2023Updated 2 years ago
- ☆13Mar 7, 2021Updated 5 years ago
- Automated and Distributed Population Genetic Model Inference from Allele Frequency Spectra☆18Updated this week
- Topology weighting from unphased genotypes of any ploidy☆23Dec 16, 2025Updated 2 months ago
- SMC++ infers population history from whole-genome sequence data.☆173Jan 20, 2024Updated 2 years ago
- Sampling and inference of genealogies with recombination☆53Jun 20, 2025Updated 8 months ago
- Maximum a posteriori estimate of contamination for ancient samples☆23Nov 4, 2025Updated 4 months ago
- Implementation of the multiple sequential markovian coalescent☆91Aug 5, 2025Updated 7 months ago
- A reimplementation of a classical PSMC method in python for educational purposes☆17Jul 22, 2024Updated last year
- ☆21Jan 11, 2024Updated 2 years ago
- Fast and flexible inference of the distribution of fitness effects (DFE), VCF-SFS parsing with ancestral allele and site-degeneracy annot…☆18Feb 28, 2026Updated last week
- 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
- Haplotype based scans for selection☆142Updated this week
- Fast inference of fine-scale recombination rates based on fused-LASSO☆56Feb 10, 2026Updated 3 weeks ago
- Drawing functions for Demes demographic models☆24Mar 2, 2026Updated last week
- Codon-Aware Multiple Sequence Alignments☆20Nov 15, 2024Updated last year
- mixture classification, constraint optimization, outlier detection, population structure, admixture history, and selection detection.☆88Jun 14, 2021Updated 4 years ago
- Accelerated Bayesian inference of population size history from whole genome data.☆33Sep 29, 2025Updated 5 months ago
- Infer the age of ancestral nodes in a tree sequence.☆24Feb 3, 2026Updated last month
- The SPrime program identifies variants that are introgressed from archaic populations.☆27May 21, 2022Updated 3 years ago
- SambaR: Snp datA Management and Basic Analyses in R☆32Oct 16, 2025Updated 4 months ago
- Workflow for processing Illumina sequencing runs for ancient human DNA☆25Oct 29, 2020Updated 5 years ago
- Tools for dealing with tree sequences coming to and from SLiM.☆28Updated this week
- Bayesian analysis of genomic sequence data under the multispecies coalescent model☆111Feb 17, 2026Updated 2 weeks ago
- Improved long-read assembly by preserving contained reads☆30Aug 22, 2024Updated last year
- Bayesian reconstruction of ancient DNA fragments☆30Aug 6, 2024Updated last year