Repositories list

• tskit-site

  Public
  tskit website

  HTML

  •

  Other

  •8•0•28•1•Updated Nov 24, 2024Nov 24, 2024

• tskit

  Public
  Population-scale genomics

  sciencebioinformaticsgenomics+ 3phylogeneticstree-sequencespython

  Python

  •

  MIT License

  •73•156•282•15•Updated Nov 22, 2024Nov 22, 2024

• tsbrowse

  Public
  Utilities for evaluating inferred tree sequences

  Python

  •

  MIT License

  •8•3•20•2•Updated Nov 22, 2024Nov 22, 2024

• tstrait

  Public
  Quantitative trait simulation for ARGs

  argstskittree-sequences

  Python

  •

  MIT License

  •6•8•2•1•Updated Nov 20, 2024Nov 20, 2024

• tszip

  Public
  Gzip-like compression for tskit tree sequences

  compressiontree-sequencetskit

  Python

  •

  MIT License

  •7•4•5•0•Updated Nov 20, 2024Nov 20, 2024

• tsdate

  Public
  Infer the age of ancestral nodes in a tree sequence.

  Python

  •

  MIT License

  •10•19•51•6•Updated Nov 20, 2024Nov 20, 2024

• tsinfer

  Public
  Infer a tree sequence from genetic variation data.

  C

  •

  GNU General Public License v3.0

  •13•56•119•6•Updated Nov 20, 2024Nov 20, 2024

• msprime

  Public
  Simulate genealogical trees and genomic sequence data using population genetic models

  pythongenomicsgenetics+ 5simulationtreescoalescenttskitmsprime

  Python

  •

  GNU General Public License v3.0

  •88•177•73•10•Updated Nov 20, 2024Nov 20, 2024

• tskit-rust

  Public
  Rust bindings for the tskit library

  rust-bindingstskittree-sequences+ 1rust

  C

  •

  MIT License

  •3•15•12•13•Updated Nov 1, 2024Nov 1, 2024

• tutorials

  Public
  A set of tutorials for msprime and tskit.

  Jupyter Notebook

  •

  Creative Commons Attribution 4.0 International

  •15•18•26•3•Updated Sep 20, 2024Sep 20, 2024

• pyslim

  Public
  Tools for dealing with tree sequences coming to and from SLiM.

  Python

  •

  MIT License

  •23•27•32•1•Updated Aug 4, 2024Aug 4, 2024

• what-is-an-arg-paper

  Public
  Manuscript and code for the "What is an ARG?" paper

  TeX

  •8•2•0•0•Updated Jun 26, 2024Jun 26, 2024

• kastore

  Public
  The key-array store for read-only numerical data.

  C

  •

  MIT License

  •7•2•5•0•Updated Jun 25, 2024Jun 25, 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

  •1•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

  •201•0•0•0•Updated Jul 13, 2023Jul 13, 2023

• tsconvert

  Public
  Utilities for converting tree sequences to and from other formats

  Python

  •

  MIT License

  •6•7•20•1•Updated Apr 18, 2023Apr 18, 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•10•2•Updated Oct 21, 2022Oct 21, 2022

• msprime-1.0-paper

  Public archive
  Publication describing msprime 1.0

  TeX

  •20•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

  •0•0•0•0•Updated Nov 28, 2020Nov 28, 2020

• msprime-asv

  Public
  Airspeed velocity site for msprime

  0•0•0•0•Updated Nov 25, 2020Nov 25, 2020

• .github

  Public
  Defaults for github shared across tskit-dev repositories

  0•0•1•0•Updated Sep 28, 2020Sep 28, 2020

• tsviz

  Public
  Visualisation tools for tree sequences

  Python

  •

  MIT License

  •3•5•8•0•Updated Sep 28, 2020Sep 28, 2020

• tscompare

  Public
  Utilities for comparing tree sequences

  MIT License

  •0•2•2•0•Updated Sep 28, 2020Sep 28, 2020