shenglin-liu / vcf2sfsView external linksLinks
R functions for generating site frequency spectra (SFS) from a VCF file.
☆28Feb 13, 2020Updated 6 years ago
Alternatives and similar repositories for vcf2sfs
Users that are interested in vcf2sfs are comparing it to the libraries listed below
Sorting:
- A collection of tools useful for preparing or manipulating site-frequency spectrum (SFS) files☆21Mar 20, 2023Updated 2 years ago
- Tools for F1 hybrid PSMC (hPSMC) divergence time inference from whole genomes☆14May 29, 2024Updated last year
- Scripts to analyze data using TreeMix. This pipeline runs TreeMix with bootstrapping, helps choose number of migration events and creates…☆42Mar 7, 2024Updated last year
- Tutorials on evolutionary genomics☆46Mar 11, 2022Updated 3 years ago
- ☆24Jun 9, 2017Updated 8 years ago
- ☆16Jan 6, 2022Updated 4 years ago
- Site frequency spectrum estimation based on window expectation-maximisation algorithm☆14May 19, 2023Updated 2 years ago
- ☆12Mar 3, 2023Updated 2 years ago
- Simple pipeline to go from an alignment to a neutral model, using the PHAST toolkit☆11Jan 17, 2020Updated 6 years ago
- Effective selection of population size projection for construction of the site frequency spectrum. Convert VCF to dadi/fastsimcoal style …☆168Aug 8, 2024Updated last year
- DFOIL: Introgression Testing for Five Taxa☆33May 15, 2021Updated 4 years ago
- ☆31Jun 15, 2023Updated 2 years ago
- Useful bioinformatic scripts☆60Nov 26, 2024Updated last year
- A tool for estimating time-dependent migration rates based on cross-/within-population coalescent rates from MSMC☆16Apr 6, 2025Updated 10 months ago
- Repository for pipeline code☆26Feb 28, 2024Updated last year
- An accessible and flexible tool for fitting demographic models with dadi using custom or published models (available here), conducting go…☆67Apr 25, 2024Updated last year
- Scripts used in the annotation of B10K genomes☆15Jun 1, 2020Updated 5 years 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
- Infer demographic history with the Moran model☆51Jun 14, 2025Updated 8 months ago
- Assemble and following pipeline used in wisent genome paper.☆17Dec 23, 2016Updated 9 years ago
- Main scripts and commands used to analyze goat population genetic and domestication☆19Mar 25, 2019Updated 6 years ago
- An R Package to build and simulate coalescent models☆20Updated this week
- Tools and Utilities for msmc and msmc2☆50Jan 23, 2026Updated 3 weeks ago
- SMC++ infers population history from whole-genome sequence data.☆172Jan 20, 2024Updated 2 years ago
- Genome Analysis Workshop (Jena 2016) material☆18Mar 3, 2017Updated 8 years ago
- Archive of Online Practical Materials for the book of Modern Phylogenetic Comparative Methods (ed. Garamszegi, 2014)☆21Jun 16, 2023Updated 2 years ago
- D Frequency Spectrum: Signatures of introgression across the allele frequency spectrum☆19Sep 19, 2020Updated 5 years ago
- Fast calculation of Patterson's D (ABBA-BABA) and the f4-ratio statistics across many populations/species☆183Dec 19, 2024Updated last year
- Inferring natural selection by comparative population genomic analysis across species☆25Oct 31, 2023Updated 2 years ago
- Drawing functions for Demes demographic models☆24Feb 2, 2026Updated 2 weeks ago
- Identification of conserved non-coding sequences in plants☆32Feb 4, 2026Updated last week
- Population genetic simulations in R☆63Jan 28, 2026Updated 2 weeks ago
- satMiner: A Toolkit to NGS satellite DNA mining and analysis☆11Mar 10, 2022Updated 3 years ago
- A Snakefile to parallelize bwa.☆13Oct 25, 2013Updated 12 years ago
- Renames headers in FASTA file☆12Jun 28, 2017Updated 8 years ago
- A coalescent simulator for genome-scale sequences☆44Jan 2, 2024Updated 2 years ago
- Daily usage script recording☆12Jan 17, 2026Updated 3 weeks ago
- The stairway plot is a method for inferring detailed population demographic history using the site frequency spectrum (SFS) from DNA sequ…☆61Sep 19, 2025Updated 4 months ago
- Set of scripts to manupulate tab-delimited genotype calls files as well as to convert calls-files to other popular formats.☆10Jan 11, 2021Updated 5 years ago