The SPrime program identifies variants that are introgressed from archaic populations.
☆27May 21, 2022Updated 3 years ago
Alternatives and similar repositories for sprime
Users that are interested in sprime are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- A statistical framework for reference-free inference of archaic local ancestry☆16Nov 8, 2019Updated 6 years ago
- D Frequency Spectrum: Signatures of introgression across the allele frequency spectrum☆19Sep 19, 2020Updated 5 years ago
- ☆48Oct 17, 2025Updated 5 months ago
- Sampling and manipulating genome-wide ancestral recombination graphs (ARGs)☆14May 1, 2023Updated 2 years ago
- Infer demographic history with the Moran model☆51Jun 14, 2025Updated 9 months ago
- ☆34Nov 11, 2025Updated 4 months ago
- Tools for identifying introgressed archaic sequence.☆12Jun 20, 2017Updated 8 years ago
- Bayesian reconstruction of ancient DNA fragments☆30Aug 6, 2024Updated last year
- The hap-ibd program detects identity-by-descent segments in phased genotype data.☆54Jun 11, 2024Updated last year
- mixture classification, constraint optimization, outlier detection, population structure, admixture history, and selection detection.☆88Jun 14, 2021Updated 4 years ago
- Module for analysing admixture graphs☆28Apr 30, 2018Updated 7 years ago
- The GitHub for CLUES2, a method for inferring and evaluating evidence for selection.☆18Apr 9, 2025Updated 11 months ago
- Fast inference of fine-scale recombination rates based on fused-LASSO☆56Feb 10, 2026Updated last month
- SMTpred is a program which combines SNP effects or individual scores from multiple traits according to their sample size, SNP-heritabilit…☆15May 25, 2017Updated 8 years ago
- ☆21Oct 2, 2024Updated last year
- A software package for local ancestry inference and haplotype phasing☆45Apr 20, 2023Updated 2 years ago
- Maximum a posteriori estimate of contamination for ancient samples☆23Nov 4, 2025Updated 4 months ago
- Infer the age of ancestral nodes in a tree sequence.☆25Updated this week
- Phase reads, assemble haplotypes and detect SVs☆19Nov 11, 2020Updated 5 years ago
- Topology weighting from unphased genotypes of any ploidy☆23Updated this week
- 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
- Faster multispecies coalescent inference using multilocus data☆14Aug 13, 2023Updated 2 years ago
- IBD based kinship estimation☆16Mar 3, 2023Updated 3 years ago
- Presentations from the course☆39Aug 28, 2023Updated 2 years ago
- A set of tools for modelling ancestry patterns along the genome.☆24Mar 13, 2026Updated last week
- The stairway plot is a method for inferring detailed population demographic history using the site frequency spectrum (SFS) from DNA sequ…☆66Sep 19, 2025Updated 6 months ago
- Infer a tree sequence from genetic variation data.☆62Updated this week
- (Greetings_here_is_yet_another) Rate of Adaptive Protein Evolution Software☆10Jul 19, 2024Updated last year
- Simulation of Epistasis Local adaptation, with Ancestry and Mate choice☆11Apr 22, 2023Updated 2 years ago
- Identity-by-descent inference using the templated positional Burrows-Wheeler transform (TPBWT)☆47Feb 23, 2026Updated last month
- ☆13Apr 30, 2019Updated 6 years ago
- ARG-based inference of selection using deep learning☆17Aug 31, 2023Updated 2 years ago
- Combine structural variation outputs from long sequencing reads into a superior call set☆18Aug 6, 2025Updated 7 months ago
- Efficient program for calculating Extended Haplotype Homozygosity (EHH) and Integrated Haplotype Score (iHS)☆45Oct 24, 2019Updated 6 years ago
- ☆15Dec 3, 2024Updated last year
- Drawing functions for Demes demographic models☆25Mar 16, 2026Updated last week
- Program to simulate admixture between multiple populations☆19Mar 8, 2023Updated 3 years ago
- A library of standard population genetic models☆139Updated this week
- Automatically exported from code.google.com/p/malder☆11Mar 17, 2015Updated 11 years ago