Automated pipeline for running CoalHMM
☆13Jan 9, 2026Updated 2 months ago
Alternatives and similar repositories for autocoalhmm
Users that are interested in autocoalhmm are comparing it to the libraries listed below
Sorting:
- Inferring natural selection by comparative population genomic analysis across species☆26Oct 31, 2023Updated 2 years ago
- Method used in the study on germline mutation rate estimation in 68 species of vertebrates.☆16Oct 11, 2021Updated 4 years ago
- ☆21Dec 13, 2024Updated last year
- 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
- TGSFilter: An ultra-fast and efficient tool for long reads filtering and trimming☆26May 18, 2024Updated last year
- Telomere local assembly, Improved whole genome polish, and Plastid assembly☆22Apr 25, 2025Updated 10 months ago
- PanEffect is a JavaScript framework to explore variant effects across a pangenome. The tool has two views that allows a user to (1) expl…☆13Jan 30, 2024Updated 2 years ago
- Integrating long read sequencing enhances short read-based locus-specific transposable element quantification☆10May 12, 2025Updated 9 months ago
- ☆41Jun 8, 2023Updated 2 years ago
- A pipeline for genomic variant detection with genome assemblies at population scale☆36Jun 3, 2025Updated 9 months ago
- Compares pangenome graphs by calculating the segmentation distance between two GFA (Graphical Fragment Assembly) files.☆13Oct 1, 2025Updated 5 months ago
- lace up GFA files using panSN path name sub-ranges to coordinate the lacing☆14Jul 30, 2025Updated 7 months ago
- Genotyping lots of samples with big pangenomes☆11Oct 30, 2025Updated 4 months ago
- Everything but the kitchen sink☆12Feb 6, 2025Updated last year
- a precise pangenome browser combining linear and graph-based pan-genome☆13Jul 16, 2024Updated last year
- A toolkit for exploring regions of variation in pangenomes☆14Feb 14, 2026Updated 3 weeks ago
- HaploSweep is a method for detecting and categorizing soft and hard selective sweeps based on haplotype structure.☆11Sep 24, 2024Updated last year
- ☆13Sep 11, 2025Updated 5 months ago
- Scripts for Wang et al (2020) Evidence for widespread selection in shaping the genomic landscape during speciation of Populus.☆11Feb 15, 2020Updated 6 years ago
- Genealogical Estimation of Variant Age (GEVA)☆32Sep 30, 2021Updated 4 years ago
- Genome-wide scan for balancing selection using beta statistic☆32Apr 26, 2023Updated 2 years ago
- Genome Assembly Validation via Inter-SUNK distances in ONT reads☆15Feb 20, 2023Updated 3 years ago
- ANI based satellite annotation☆24Mar 2, 2026Updated last week
- ☆14Apr 26, 2023Updated 2 years ago
- An R package for comparative transcriptomic analyses of hybrids and their progenitors☆15Sep 5, 2024Updated last year
- Lightweight mosaic/somatic SV caller for long reads (WIP)☆35Oct 27, 2025Updated 4 months 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
- Invertory of TE-gene isoforms☆14Sep 18, 2023Updated 2 years ago
- Time-stratified f-statistics☆15Aug 1, 2025Updated 7 months ago
- Prepare XML input files for divergence-time estimation with SNAPP☆20Dec 3, 2022Updated 3 years ago
- 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…☆44Mar 7, 2024Updated 2 years ago
- Kmer Analysis of Pileups for Genotyping☆37Updated this week
- Rust package for constructing and analyzing phylogenies. (unpolished & unmaintained)☆15May 1, 2025Updated 10 months ago
- PAF (pairwise alignment format) validator based on extended CIGAR strings☆15Aug 10, 2025Updated 6 months ago
- Repository for the 2017 Genome Biology publication, "The interplay of demography and selection during maize domestication and expansion"☆17Nov 24, 2020Updated 5 years ago
- ☆15Jun 29, 2021Updated 4 years ago
- MEMO: MEM-based pangenome indexing for k-mer queries☆20Jun 11, 2024Updated last year
- The GitHub for CLUES2, a method for inferring and evaluating evidence for selection.☆18Apr 9, 2025Updated 11 months ago