tools.yaml

# Gathered using a mixture of
# - looking up deps.dev for tskit/msprime
# - inspecting GitHub dependents graph
# - looking up conda dependents using script conda_lookup.py

- name: Lorax
  repo: https://github.com/pratikkatte/lorax/
  interface: Python
  type: visualisation
  publication: https://doi.org/10.64898/2026.02.19.706861
  package: pip
  notes: Interactive visualization and exploration of Ancestral Recombination Graphs (ARGs)
  implementation: Python,JavaScript
  
- name: Moonshine.jl
  repo: https://github.com/ps-pat/Moonshine.jl
  interface: Python
  type: arg_inference
  publication: https://doi.org/10.3389/fgene.2026.1753780
  package: julia
  notes: Uses msprime; available at https://juliahub.com/ui/Packages/General/Moonshine
  implementation: Julia

- name: Terracotta
  repo: https://github.com/kitchensjn/terracotta
  interface: Python
  type: popgen_inf
  note: In development
  implementation: Python

- name: CLUES2
  repo: https://github.com/avaughn271/CLUES2
  interface: Python
  type: popgen_inf
  publication: https://doi.org/10.1371/journal.pgen.1008384
  note: tskit is only used to convert SINGER output to CLUES format
  implementation: Python

- name: tskibd
  repo: https://github.com/bguo068/tskibd
  interface: C
  type: analysis
  publication: https://doi.org/10.1038/s41467-024-46659-0
  implementation: C++

- name: tslmm
  repo: https://github.com/hanbin973/tslmm
  interface: Python
  type: statgen_inf
  package: pip, guix
  publication: https://doi.org/10.1101/2025.07.14.664631
  implementation: Python

- name: bio2zarr
  repo: https://github.com/sgkit-dev/bio2zarr
  interface: Python
  type: analysis
  package: pypi, conda, guix
  publication: https://doi.org/10.1093/gigascience/giaf049
  implementation: Python

- name: grgl
  repo: https://github.com/aprilweilab/grgl
  interface: C
  type: analysis
  package: conda, pip
  publication: https://doi.org/10.1038/s43588-024-00739-9
  notes: Conversion from tskit ``grg convert /path/to/my.trees my.grg``. The python package is called pygrgl.
  implementation: C++

- name: gfkit
  repo: https://github.com/lukashuebner/gfkit
  interface: C
  type: analysis
  publication: https://doi.org/10.4230/LIPIcs.WABI.2024.5
  notes: Uses tskit as its input format
  implementation: C++

- name: gIMble
  repo: https://github.com/LohseLab/gIMble
  interface: Python
  type: popgen_inf
  package: conda, pip
  publication: https://doi.org/10.1371/journal.pgen.1010999
  implementation: Python

- name: ipcoal
  repo: https://github.com/eaton-lab/ipcoal
  interface: Python
  type: simulation
  package: conda, pip
  publication: https://doi.org/10.1093/bioinformatics/btaa486
  implementation: Python

- name: shadie
  repo: https://github.com/elissasoroj/shadie
  interface: Python
  type: simulation
  package: conda, pip
  implementation: Python

- name: necsim-rust
  repo: https://github.com/juntyr/necsim-rust
  interface: Rust
  type: simulation
  package: cargo
  publication: https://doi.org/10.48550/arXiv.2108.05815
  implementation: Rust

- name: lineagekit
  repo: https://github.com/lineagekit/lineagekit
  interface: Python
  type: analysis
  package: pip
  note: Unclear if there's much functionality here yet
  implementation: Python

- name: gaia
  repo: https://github.com/blueraleigh/gaia
  interface: C
  type: popgen_inf
  publication: https://doi.org/10.1126/science.adp4642
  implementation: R,C

- name: gaiapy
  repo: https://github.com/chris-a-talbot/gaiapy
  package: pip, guix
  interface: Python
  type: popgen_inf
  note: Reimplementation of gaia R package.
  implementation: Python

- name: fastgaia
  repo: https://github.com/chris-a-talbot/fastgaia
  package: pip, guix
  interface: Python
  type: popgen_inf
  implementation: Python

- name: espalier
  repo: https://github.com/davidrasm/Espalier
  package: pip
  interface: Python
  type: arg_inference
  publication: https://doi.org/10.1093/sysbio/syad040
  implementation: Python

- name: GADMA
  repo: https://github.com/ctlab/gadma
  package: pip, conda
  interface: Python
  type: popgen_inf
  publication: https://doi.org/10.1093/gigascience/giad059
  implementation: Python

- name: spaceprime
  repo: https://github.com/connor-french/spaceprime
  package: pip
  interface: Python
  type: simulation
  implementation: Python

- name: arg-lmm
  repo: https://github.com/PalamaraLab/arg-lmm
  package: pip
  interface: Python
  type: statgen_inf
  publication: https://doi.org/10.1016/j.xgen.2025.101072
  implementation: Python

- name: transmission
  repo: https://github.com/mpjuers/transmission
  package: pip
  interface: Python
  type: popgen_inf
  implementation: Python

- name: ReLERNN
  repo: https://github.com/kr-colab/ReLERNN
  package: pip
  interface: Python
  type: popgen_inf
  publication: https://doi.org/10.1093/molbev/msaa038
  implementation: Python

- name: momi2
  repo: https://github.com/popgenmethods/momi2
  package: pip
  interface: Python
  type: popgen_inf
  publication: https://doi.org/10.1080/01621459.2019.1635482
  implementation: Python

- name: dnadna
  repo: https://gitlab.com/mlgenetics/dnadna
  package: pip, conda
  interface: Python
  type: popgen_inf
  publication: https://doi.org/10.1093/bioinformatics/btac765
  implementation: Python

- name: dinf
  repo: https://github.com/racimolab/dinf
  package: pip, conda
  interface: Python
  type: popgen_inf
  publication: https://doi.org/10.1101/2023.04.27.538386
  implementation: Python

- name: DISMaL
  repo: https://github.com/simonharnqvist/DISMaL
  package: pip
  interface: Python
  type: popgen_inf
  publication: https://doi.org/10.1016/j.tpb.2021.03.001
  implementation: Python

- name: disperseNN2
  repo: https://github.com/kr-colab/disperseNN2
  package: pip
  interface: Python
  type: popgen_inf
  publication: https://doi.org/10.1186/s12859-023-05522-7
  implementation: Python

- name: adnator
  repo: https://github.com/jazpy/adnator
  package: pip
  interface: Python
  type: simulation
  implementation: Python,C++

- name: cnasim
  repo: https://github.com/samsonweiner/cnasim
  package: pip, conda
  interface: Python
  type: simulation
  publication: https://doi.org/10.1093/bioinformatics/btad434
  implementation: Python

- name: msprime
  repo: https://github.com/tskit-dev/msprime
  # publication: https://doi.org/10.1093/genetics/iyab229
  publication: https://doi.org/10.1371/journal.pcbi.1004842
  interface: C, Python
  package: pip, conda, guix
  type: simulation
  implementation: Python,C

- name: pyslim
  repo: https://github.com/tskit-dev/pyslim
  publication: https://doi.org/10.1101/2025.09.30.679676
  type: simulation
  package: pip, conda, guix
  interface: Python
  implementation: Python

- name: tstrait
  repo: https://github.com/tskit-dev/tstrait
  publication: https://doi.org/10.1093/bioinformatics/btae334
  interface: Python
  type: simulation
  package: pip, conda, guix
  implementation: Python

- name: SLiM
  repo: https://github.com/MesserLab/SLiM
  publication: https://doi.org/10.1093/molbev/msy228
  interface: C
  type: simulation
  package: conda, guix
  implementation: C++,C

- name: fwdpy11
  repo: https://github.com/molpopgen/fwdpy11
  publication: https://doi.org/10.1534/genetics.119.302662
  interface: C, Python
  package: pip, conda, guix
  type: simulation
  implementation: C++,Python

- name: stdpopsim
  repo: https://github.com/popsim-consortium/stdpopsim
  publication: https://doi.org/10.7554/eLife.54967
  interface: Python
  package: pip, conda, guix
  type: simulation
  implementation: Python

- name: RADinitio
  repo: https://catchenlab.life.illinois.edu/radinitio/
  publication: https://doi.org/10.1111/1755-0998.13163
  interface: Python
  package: pip
  type: simulation
  note: No repo, homepage
  implementation: Python

- name: slendr
  repo: https://github.com/bodkan/slendr/
  publication: https://doi.org/10.24072/pcjournal.354
  interface: Python
  package: CRAN
  type: simulation
  implementation: R

- name: gridCoal
  repo: https://github.com/Trubenova/gridCoal
  publication: https://doi.org/10.1111/1755-0998.13676
  interface: Python
  type: simulation
  implementation: Python

- name: Geonomics
  repo: https://github.com/drewhart/geonomics
  publication: https://doi.org/10.1093/molbev/msab175
  interface: Python
  package: pip, conda
  type: simulation
  implementation: Python

- name: TwisstNTern
  repo: https://github.com/HilaLifchitz/TwisstNTern
  publication: https://doi.org/10.32942/X29941
  type: simulation
  interface: Python
  notes: Not primarly simulator, but includes a frontend for running msprime simulations.
  package: guix
  implementation: Python

- name: tsinfer
  repo: https://github.com/tskit-dev/tsinfer
  publication: https://doi.org/10.1038/s41588-019-0483-y
  interface: C, Python
  package: pip, conda, guix
  type: arg_inference
  implementation: C,Python

- name: sc2ts
  repo: https://github.com/tskit-dev/sc2ts
  publication: https://doi.org/10.1101/2023.06.08.544212
  interface: Python
  package: pip, guix
  type: arg_inference
  implementation: Python

- name: tsdate
  repo: https://github.com/tskit-dev/tsdate
  publication: https://doi.org/10.1126/science.abi8264
  interface: Python
  type: arg_inference
  package: pip, conda, guix
  implementation: Python

- name: Relate
  repo: https://github.com/MyersGroup/relate
  publication: https://doi.org/10.1038/s41588-019-0484-x
  type: arg_inference
  interface: C
  notes: Strictly, relate_lib converts to tskit, but seems like hair-splitting
  package: guix
  implementation: C++

- name: Colate
  repo: https://github.com/leospeidel/Colate
  publication: https://doi.org/10.1093/molbev/msab174
  type: popgen_inf
  interface: C
  notes: Definitely compiled into Colate binary
  implementation: C++

- name: ARGneedle
  repo: https://github.com/palamaralab/arg-needle
  publication: https://doi.org/10.1038/s41588-023-01379-x
  interface: Python
  package: pip
  type: arg_inference
  implementation: Python,C++

- name: Threads
  repo: https://github.com/palamaralab/threads
  publication: https://doi.org/10.1101/2024.08.31.610248
  interface: Python
  package: pip, guix
  type: arg_inference
  implementation: C++,Python

- name: sticcs
  repo: https://github.com/simonhmartin/sticcs
  publication: https://doi.org/10.1093/genetics/iyaf181
  interface: Python
  type: arg_inference
  package: pip
  implementation: Python

- name: ARGinfer
  repo: https://github.com/alimahmoudi29/arginfer
  publication: https://doi.org/10.1371/journal.pcbi.1009960
  interface: Python
  package: pip
  type: arg_inference
  implementation: Python

- name: SINGER
  repo: https://github.com/popgenmethods/SINGER
  publication: https://doi.org/10.1038/s41588-025-02317-9
  interface: Python
  type: arg_inference
  package: guix
  implementation: C++,Python

- name: POLEGON
  repo: https://github.com/YunDeng98/POLEGON
  publication: https://doi.org/10.1073/pnas.2504461122
  type: arg_inference
  interface: Python
  package: guix
  implementation: C++,Python

- name: mrpast
  repo: https://github.com/aprilweilab/mrpast
  publication: https://doi.org/10.1101/2025.10.07.680347
  type: popgen_inf
  package: pip, conda
  interface: Python
  implementation: C++,Python

- name: phlash
  repo: https://github.com/jthlab/phlash
  publication: https://doi.org/10.1038/s41588-025-02323-x
  type: popgen_inf
  package: pip
  interface: Python
  implementation: Python

- name: spacetrees
  repo: https://github.com/osmond-lab/spacetrees
  publication: https://doi.org/10.7554/eLife.72177
  type: popgen_inf
  interface: Python
  implementation: Python

- name: sparg
  repo: https://github.com/osmond-lab/sparg
  publication: https://doi.org/10.1093/g3journal/jkaf214
  type: popgen_inf
  package: pip, guix
  interface: Python
  implementation: Python

- name: mapNN
  repo: https://github.com/kr-colab/mapNN
  publication: https://doi.org/10.1111/1755-0998.14005
  type: popgen_inf
  interface: Python
  implementation: Python

- name: tsbrowse
  repo: https://github.com/tskit-dev/tsbrowse
  publication: https://doi.org/10.1093/bioinformatics/btaf393
  type: visualisation
  package: pip, guix
  interface: Python
  implementation: Python

- name: tskit-arg-visualizer
  repo: https://github.com/kitchensjn/tskit_arg_visualizer
  publication: https://doi.org/10.1093/bioadv/vbaf302
  type: visualisation
  package: pip, guix
  interface: Python
  implementation: Python,JavaScript

- name: ARGscape
  repo: https://github.com/chris-a-talbot/argscape
  publication: https://doi.org/10.48550/arXiv.2510.07255
  type: visualisation
  package: pip, guix
  interface: Python
  implementation: TypeScript,Python

- name: tscompare
  repo: https://github.com/tskit-dev/tscompare
  publication: https://doi.org/10.1093/genetics/iyaf198
  type: analysis
  package: pip, guix
  interface: Python
  implementation: Python

- name: tspop
  repo: https://github.com/gtsambos/tspop
  publication: https://doi.org/10.1093/bioadv/vbad163
  type: analysis
  package: pip, guix
  interface: Python
  implementation: Python

- name: twisst2
  repo: https://github.com/simonhmartin/twisst2
  publication: https://doi.org/10.1093/genetics/iyaf181
  type: analysis
  interface: Python
  package: pip
  implementation: Python

- name: phylokit
  repo: https://github.com/jeromekelleher/phylokit
  interface: Python
  type: analysis
  note: In development experimental phylogenetics toolkit with a conversion from/to tskit trees.
  implementation: Python

- name: egrm
  repo: https://github.com/Ephraim-usc/egrm
  publication: https://doi.org/10.1016/j.ajhg.2022.03.016
  type: statgen_inf
  package: pip
  interface: Python
  implementation: Python,C

- name: as-eGRM
  repo: https://github.com/jitang-github/asegrm
  publication: https://doi.org/10.1016/j.ajhg.2025.06.016
  type: statgen_inf
  interface: Python
  package: pip
  implementation: Python,C

- name: lgdm
  repo: https://github.com/awohns/ldgm
  publication: https://doi.org/10.1038/s41588-023-01487-8
  type: statgen_inf
  package: pip
  interface: Python
  implementation: Python,Matlab

- name: SCAR
  repo: https://github.com/sunnyfangfangguo/SCAR_project_repo
  publication: https://doi.org/10.1371/journal.pcbi.1010422
  type: popgen_inf
  interface: Python
  implementation: Python

- name: gLike
  repo: https://github.com/Ephraim-usc/glike
  publication: https://doi.org/10.1038/s41588-025-02129-x
  type: popgen_inf
  interface: Python
  package: pip
  implementation: Python,C

- name: dolores
  repo: https://github.com/a-ignatieva/dolores
  publication: https://doi.org/10.1093/molbev/msaf190
  type: popgen_inf
  interface: Python
  implementation: Python

- name: spectre
  repo: https://github.com/a-ignatieva/spectre
  publication: https://doi.org/10.1093/genetics/iyaf184
  type: popgen_inf
  interface: Python
  implementation: Python

- name: coaldecoder
  repo: https://github.com/nspope/coaldecoder
  publication: https://doi.org/10.1073/pnas.2208116120
  type: popgen_inf
  interface: Python
  notes: Presented as an R package, but not on CRAN.
  # Dropping Python here as cols are too wide
  implementation: C++,R

- name: RcppTskit
  repo: https://github.com/HighlanderLab/RcppTskit
  interface: C, R
  type: analysis
  note: R package providing access to the tskit C API for high-performance/low-level use cases.
  implementation: R,C,C++