A statistical framework for reference-free inference of archaic local ancestry
☆16Nov 8, 2019Updated 6 years ago
Alternatives and similar repositories for ArchIE
Users that are interested in ArchIE are comparing it to the libraries listed below
Sorting:
- ☆32Jan 5, 2023Updated 3 years ago
- Ancestry_HMM-S is program designed to infer adaptive introgression from population genomic data☆19Sep 25, 2023Updated 2 years ago
- The SPrime program identifies variants that are introgressed from archaic populations.☆27May 21, 2022Updated 3 years ago
- Faster multispecies coalescent inference using multilocus data☆14Aug 13, 2023Updated 2 years ago
- Source code for the program MavericK, described fully at www.bobverity.com/maverick☆12Jun 21, 2018Updated 7 years ago
- ☆34Jan 14, 2026Updated last month
- Software for detecting introgression using supervised machine learning☆21Nov 21, 2022Updated 3 years ago
- Sampling and manipulating genome-wide ancestral recombination graphs (ARGs)☆14May 1, 2023Updated 2 years ago
- The flare program performs local ancestry inference☆46Nov 4, 2025Updated 4 months ago
- ☆15Mar 20, 2023Updated 2 years ago
- ☆15Jul 17, 2019Updated 6 years ago
- ☆48Oct 17, 2025Updated 4 months ago
- Process MS results in R, in a tidy way☆16May 25, 2018Updated 7 years ago
- Minimal Assumption Genomic Inference of Coalescence☆14Aug 8, 2023Updated 2 years ago
- Haplotype and population structure inference using neural networks.☆28Dec 5, 2024Updated last year
- Method for dating admixture in ancient DNA specimens☆28Jan 12, 2022Updated 4 years ago
- Predicts adaptive introgression using a CNN trained on genotype matrices.☆17Nov 28, 2023Updated 2 years ago
- The GitHub for CLUES2, a method for inferring and evaluating evidence for selection.☆18Apr 9, 2025Updated 10 months ago
- ☆30Oct 14, 2022Updated 3 years ago
- Framework for analyzing low depth NGS data in heterogeneous populations using PCA.☆59Jun 27, 2025Updated 8 months ago
- ☆20Sep 10, 2020Updated 5 years ago
- D Frequency Spectrum: Signatures of introgression across the allele frequency spectrum☆19Sep 19, 2020Updated 5 years ago
- Maximum a posteriori estimate of contamination for ancient samples☆23Nov 4, 2025Updated 4 months ago
- A package for population structure inference from RAD-seq data☆34May 14, 2021Updated 4 years ago
- Quantifying Introgression via Branch Lengths☆56Sep 30, 2022Updated 3 years ago
- 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
- mixture classification, constraint optimization, outlier detection, population structure, admixture history, and selection detection.☆88Jun 14, 2021Updated 4 years ago
- Work for the tree sequence inference paper.☆23Oct 19, 2020Updated 5 years ago
- Infer the age of ancestral nodes in a tree sequence.☆24Feb 3, 2026Updated last month
- An Expectation-Maximization algorithm to infer mutational signatures☆26Nov 16, 2016Updated 9 years ago
- Analysis of inference methods on standard population models☆25Dec 3, 2021Updated 4 years ago
- Tutorial for visualising admixture on a map☆24Jan 4, 2021Updated 5 years ago
- (a) (p)erfect (c)ircle? ... tests DNA sequences for overlapping ends, then trims and rejoins, and aligns reads to test the join☆11Apr 29, 2021Updated 4 years ago
- Demographic inference from whole genomes☆13Oct 18, 2022Updated 3 years ago
- Fitting latent factor mixed models☆13Jun 12, 2020Updated 5 years ago
- Estimate population history parameters from site pattern frequencies.☆12Dec 2, 2025Updated 3 months ago
- (Greetings_here_is_yet_another) Rate of Adaptive Protein Evolution Software☆10Jul 19, 2024Updated last year
- A utility for splitting mixed origin NGS reads☆10Jun 1, 2021Updated 4 years ago
- ☆15Dec 3, 2024Updated last year