ruidlpm / pathPhynderView external linksLinks
A workflow for integrating ancient lineages into present-day phylogenies.
☆32Jul 7, 2025Updated 7 months ago
Alternatives and similar repositories for pathPhynder
Users that are interested in pathPhynder are comparing it to the libraries listed below
Sorting:
- Workflow for processing Illumina sequencing runs for ancient human DNA☆25Oct 29, 2020Updated 5 years ago
- This project is a collection of tools for bioinformatic processing of ancient DNA data at the Harvard Medical School Reich Lab.☆26Aug 15, 2025Updated 5 months ago
- Time-stratified f-statistics☆15Aug 1, 2025Updated 6 months ago
- Yleaf software for human Y-chromosomal haplogroup inference from next generation sequencing data☆32Mar 18, 2025Updated 10 months ago
- Python package for detecting positive selective sweeps using time-series genomics sampling data.☆19Apr 9, 2024Updated last year
- ☆11Jun 26, 2020Updated 5 years ago
- Sampling and manipulating genome-wide ancestral recombination graphs (ARGs)☆14May 1, 2023Updated 2 years ago
- ☆22Jun 9, 2021Updated 4 years ago
- BITE: BioInformatics tools for everyone☆21Jul 25, 2024Updated last year
- ☆51Jan 28, 2026Updated 2 weeks ago
- Maximum a posteriori estimate of contamination for ancient samples☆23Nov 4, 2025Updated 3 months ago
- Estimation of pairwise distances under a probabilistic framework☆11Aug 11, 2023Updated 2 years ago
- An R package to perform systematic quality checks on comparative genomics analyses☆12Jan 12, 2024Updated 2 years ago
- YFull YTree☆14Dec 26, 2025Updated last month
- LaTeX Template for Fudan University School of Computer Science 2024☆11May 21, 2024Updated last year
- Heuristic search algorithm for fitting qpGraph models☆11Aug 4, 2022Updated 3 years ago
- Tools for analyzing raw DNA test data files. Shows Y chromosome and mitochondrial mtDNA haplogroups. LGPLv3 - use freely but share improv…☆13Dec 2, 2024Updated last year
- A merged read deduplication tool capable to perform merged read deduplication on single end data.☆12Sep 4, 2024Updated last year
- mapDamage: tracking and quantifying damage patterns in ancient DNA sequences☆48Jul 14, 2025Updated 7 months ago
- The index files for sequence and other data created for the 1000 Genomes project and the International Genome Sample Resource☆46Jul 15, 2019Updated 6 years ago
- Ascertained Sequentially Markovian Coalescent☆16Oct 22, 2025Updated 3 months ago
- A Swiss-Army-Knife for Bioinformaticians☆14Jan 27, 2026Updated 2 weeks ago
- Infer demographic history with the Moran model☆51Jun 14, 2025Updated 8 months ago
- ☆13Dec 3, 2024Updated last year
- ☆15Jul 21, 2022Updated 3 years ago
- Tools test whether admixture occurred and more☆219Sep 6, 2024Updated last year
- A developed pipeline for expressed endogenous retrovirus identification.☆16Oct 9, 2024Updated last year
- Method for dating admixture in ancient DNA specimens☆28Jan 12, 2022Updated 4 years ago
- A fully reproducible and state-of-the-art ancient DNA analysis pipeline☆197Jan 30, 2026Updated 2 weeks ago
- Software to call ROHs☆17Oct 15, 2025Updated 3 months ago
- An R package for comparative transcriptomic analyses of hybrids and their progenitors☆15Sep 5, 2024Updated last year
- ☆15Jun 10, 2020Updated 5 years ago
- A tool to infer species tree and phylogenetic network from multilocus data☆32Jul 2, 2020Updated 5 years ago
- A chromosomal visualization package for python.☆15Nov 21, 2023Updated 2 years ago
- 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
- Detecting IBD within low coverage ancient DNA data. Development Repository for software package that contains code for manuscript.☆14Jan 28, 2026Updated 2 weeks ago
- A tool for estimating time-dependent migration rates based on cross-/within-population coalescent rates from MSMC☆16Apr 6, 2025Updated 10 months ago
- The flare program performs local ancestry inference☆46Nov 4, 2025Updated 3 months ago
- Pinpoints the mutation favored by selection☆34Nov 2, 2021Updated 4 years ago