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    28 repositories

    • msprime

      Public
      Simulate genealogical trees and genomic sequence data using population genetic models
      pythongenomicsgeneticssimulationtreescoalescenttskitmsprime
      Python
      •
      GNU General Public License v3.0
      •89•197•74•9•Updated Sep 12, 2025Sep 12, 2025

    • kastore

      Public
      The key-array store for read-only numerical data.
      C
      •
      MIT License
      •7•2•4•1•Updated Sep 11, 2025Sep 11, 2025

    • tskit-site

      Public
      tskit website
      HTML
      •
      Other
      •4•0•24•0•Updated Sep 11, 2025Sep 11, 2025

    • .github

      Public
      Defaults for github shared across tskit-dev repositories
      1•0•1•0•Updated Sep 10, 2025Sep 10, 2025

    • tsinfer

      Public
      Infer a tree sequence from genetic variation data.
      C
      •
      GNU General Public License v3.0
      •16•60•103•6•Updated Sep 10, 2025Sep 10, 2025

    • tsbrowse

      Public
      Utilities for evaluating inferred tree sequences
      Python
      •
      MIT License
      •8•4•22•2•Updated Sep 10, 2025Sep 10, 2025

    • tscompare

      Public
      Utilities for comparing tree sequences
      Python
      •
      MIT License
      •3•2•3•0•Updated Sep 10, 2025Sep 10, 2025

    • pyslim

      Public
      Tools for dealing with tree sequences coming to and from SLiM.
      Python
      •
      MIT License
      •23•28•30•2•Updated Sep 10, 2025Sep 10, 2025

    • tskit

      Public
      Population-scale Ancestral Recombination Graph (ARG) library
      pythonsciencebioinformaticsgenomicsphylogeneticstree-sequences
      Python
      •
      MIT License
      •77•171•90•11•Updated Sep 10, 2025Sep 10, 2025

    • tszip

      Public
      Gzip-like compression for tskit tree sequences
      compressiontree-sequencetskit
      Python
      •
      MIT License
      •7•5•8•0•Updated Sep 10, 2025Sep 10, 2025

    • tstrait

      Public
      Quantitative trait simulation for ARGs
      argstskittree-sequences
      Python
      •
      MIT License
      •6•8•2•1•Updated Sep 9, 2025Sep 9, 2025

    • tsdate

      Public
      Infer the age of ancestral nodes in a tree sequence.
      Python
      •
      MIT License
      •11•22•40•3•Updated Sep 9, 2025Sep 9, 2025

    • tskit-rust

      Public
      Rust bindings for the tskit library
      rust-bindingstskittree-sequencesrust
      C
      •
      MIT License
      •5•16•12•21•Updated Sep 2, 2025Sep 2, 2025

    • tutorials

      Public
      A set of tutorials for msprime and tskit.
      Jupyter Notebook
      •
      Creative Commons Attribution 4.0 International
      •17•20•24•4•Updated Sep 1, 2025Sep 1, 2025

    • tskit-explore

      Public
      JupyterLite deployment for tskit notebooks
      Jupyter Notebook
      •1•0•0•0•Updated Jul 9, 2025Jul 9, 2025

    • genetic-relatedness-paper

      Public
      Manuscript and files for the Genetic relatedness paper
      TeX
      •0•0•2•0•Updated Apr 15, 2025Apr 15, 2025

    • tsconvert

      Public
      Utilities for converting tree sequences to and from other formats
      Python
      •
      MIT License
      •6•7•21•1•Updated Mar 19, 2025Mar 19, 2025

    • what-is-an-arg-paper

      Public archive
      Manuscript and code for the "What is an ARG?" paper
      TeX
      •8•2•0•0•Updated Jun 26, 2024Jun 26, 2024

    • tskit-build-examples

      Public
      Examples of how to build projects using tskit.
      C
      •3•1•0•1•Updated Dec 20, 2023Dec 20, 2023

    • containers

      Public
      Containerised environments for tskit and related projects
      Shell
      •
      MIT License
      •2•0•0•0•Updated Aug 4, 2023Aug 4, 2023

    • tskit-book-theme

      Public
      A book theme for documentation of tskit projects
      Jupyter Notebook
      •
      BSD 3-Clause "New" or "Revised" License
      •207•0•0•0•Updated Jul 13, 2023Jul 13, 2023

    • administrative

      Public
      project management documents and discussions for tskit development
      Makefile
      •
      GNU General Public License v3.0
      •3•1•5•0•Updated Mar 2, 2023Mar 2, 2023

    • tskit-paper

      Public
      Python
      •4•2•11•2•Updated Oct 21, 2022Oct 21, 2022

    • msprime-1.0-paper

      Public archive
      Publication describing msprime 1.0
      TeX
      •21•4•0•0•Updated Aug 24, 2022Aug 24, 2022

    • build-deploy-docs

      Public
      Github composite run steps action for building and deploying docs
      MIT License
      •0•0•0•0•Updated Jan 16, 2021Jan 16, 2021

    • tskit-docs

      Public
      HTML
      •1•0•0•0•Updated Nov 28, 2020Nov 28, 2020

    • msprime-asv

      Public
      Airspeed velocity site for msprime
      1•0•0•0•Updated Nov 25, 2020Nov 25, 2020

    • tsviz

      Public
      Visualisation tools for tree sequences
      Python
      •
      MIT License
      •4•5•8•0•Updated Sep 28, 2020Sep 28, 2020