popgenmethods / smcpp
SMC++ infers population history from whole-genome sequence data.
☆158Updated last year
Alternatives and similar repositories for smcpp:
Users that are interested in smcpp are comparing it to the libraries listed below
- Fast calculation of Patterson's D (ABBA-BABA) and the f4-ratio statistics across many populations/species☆166Updated last month
- Implementation of the Pairwise Sequentially Markovian Coalescent (PSMC) model☆159Updated 2 years ago
- A library for running k-mers based GWAS☆106Updated 3 months ago
- Software for painlessly estimating average nucleotide diversity within and between populations☆124Updated 8 months ago
- Scripts for analysis used during the course☆86Updated 9 months ago
- Effective selection of population size projection for construction of the site frequency spectrum. Convert VCF to dadi/fastsimcoal style …☆141Updated 5 months ago
- Generate an interactive dot plot from mummer or minimap alignments☆195Updated last year
- Haplotype based scans for selection☆118Updated last week
- MitoZ: A toolkit for assembly, annotation, and visualization of animal mitochondrial genomes☆120Updated 2 months ago
- PopLDdecay: a fast and effective tool for linkage disequilibrium decay analysis based on variant call format(VCF) files☆188Updated 5 months ago
- ☆80Updated 3 years ago
- A set of functions to visualise genotypes based on a VCF☆85Updated 3 years ago
- Code to compute the XP-CLR statistic to infer natural selection☆93Updated 2 years ago
- An accessible and flexible tool for fitting demographic models with dadi using custom or published models (available here), conducting go…☆63Updated 9 months ago
- RaGOO is no longer supported. Please use RagTag instead: https://github.com/malonge/RagTag☆172Updated 3 years ago
- Multi-level visualization of genomic statistical variables on rectangular chromosomes☆85Updated 2 months ago
- Version 5 of the CAFE phylogenetics software☆121Updated this week
- VCF2Dis: A new simple and efficient software to calculate p-distance matrix and construct population phylogeny based Variant Call Forma…☆84Updated 3 weeks ago
- Yet another Hi-C scaffolding tool☆138Updated 2 months ago
- Reference-free profiling of polyploid genomes☆112Updated 6 months ago
- ALLHiC: phasing and scaffolding polyploid genomes based on Hi-C data☆174Updated 3 months ago
- Ultra-fast de novo assembler using long noisy reads☆131Updated 3 years ago
- Recovering genes from targeted sequence capture data☆115Updated 3 weeks ago
- Fast and accurately polish the genome generated by long reads.☆217Updated 3 weeks ago
- Find, circularise and annotate mitogenome from PacBio assemblies☆174Updated 2 weeks ago
- MitoFinder: efficient automated large-scale extraction of mitogenomic data from high throughput sequencing data☆93Updated 9 months ago
- A new simple and efficient software to PCA and Cluster For popolation VCF File☆68Updated 3 weeks ago
- A flexible, scalable, and reproducible pipeline to automate variant calling from raw sequence reads, with lots of bells and whistles.☆95Updated last week
- a bash pipeline for RAD sequencing☆52Updated this week
- LTR_retriever is a highly accurate and sensitive program for identification of LTR retrotransposons; The LTR Assembly Index (LAI) is also…☆195Updated 3 weeks ago