tskit-dev / tskit
Population-scale genomics
☆162Updated this week
Alternatives and similar repositories for tskit:
Users that are interested in tskit are comparing it to the libraries listed below
- Simulate genealogical trees and genomic sequence data using population genetic models☆185Updated 2 weeks ago
- A library of standard population genetic models☆129Updated this week
- Software for painlessly estimating average nucleotide diversity within and between populations☆124Updated last week
- Infer a tree sequence from genetic variation data.☆57Updated this week
- Implementation of the Pairwise Sequentially Markovian Coalescent (PSMC) model☆162Updated 2 years ago
- SMC++ infers population history from whole-genome sequence data.☆159Updated last year
- Scalable genetics toolkit☆249Updated this week
- Inference of ploidy and heterozygosity structure using whole genome sequencing data☆258Updated 3 weeks ago
- A simple Snakemake profile for Slurm without --cluster-config☆150Updated 7 months ago
- Long read / genome alignment software☆272Updated 3 months ago
- Fast calculation of Patterson's D (ABBA-BABA) and the f4-ratio statistics across many populations/species☆166Updated last month
- Haplotype based scans for selection☆120Updated this week
- A flexible, scalable, and reproducible pipeline to automate variant calling from raw sequence reads, with lots of bells and whistles - fo…☆96Updated this week
- A set of functions to visualise genotypes based on a VCF☆85Updated 3 years ago
- SEER, reimplemented in python 🐍🔮☆115Updated 3 months ago
- Tool to plot synteny and structural rearrangements between genomes☆295Updated 2 months ago
- A variational framework for inferring population structure from SNP genotype data.☆135Updated 2 years ago
- Effective selection of population size projection for construction of the site frequency spectrum. Convert VCF to dadi/fastsimcoal style …☆143Updated 6 months ago
- Calculate summary statistics and manipulate multiple sequence alignments☆78Updated last year
- A fully reproducible and state-of-the-art ancient DNA analysis pipeline☆159Updated this week
- Program for analysing NGS data.☆233Updated 3 months ago
- An imagemagick-like frontend to Biopython SeqIO☆115Updated 10 months ago
- Pairwise whole genome aligner☆147Updated last month
- Tools for dealing with tree sequences coming to and from SLiM.☆27Updated 2 months ago
- Convert SNPs in VCF format to PHYLIP, NEXUS, binary NEXUS, or FASTA alignments for phylogenetic analysis☆304Updated last year
- RaGOO is no longer supported. Please use RagTag instead: https://github.com/malonge/RagTag☆172Updated 3 years ago
- A library for running k-mers based GWAS☆106Updated 3 months ago
- Long read production pipelines☆143Updated this week
- Redundans is a pipeline that assists an assembly of heterozygous/polymorphic genomes.☆137Updated last year
- A sequencing simulator☆192Updated 6 months ago