TKF-DP

Cherry-trained, indel-aware Potts coevolution model — reference implementation for the paper:

Maraschino: TKF-DP (Holmes & Large) bioRxiv preprint: 10.64898/2026.05.16.725674v1

A web-browsable version of the supplement, plus links to all code and data releases, lives at tkfdp.net.

Repository

• math-paper/ — LaTeX source for the manuscript and supplement. Build with cd math-paper && bash build.sh.
• src/tkfdp/ — Python reference implementation (TKF-DP MCMC sampler, Potts-atom DP, EM warmup).
• analysis/scripts/ — figure-generation scripts and the recipe for reproducing every cell of Tables 1 and 2.
• aws/ — SkyPilot YAMLs for large sweeps on cloud GPUs.
• math-paper/tkf-mixdom/ (git submodule) — JAX implementation of TKF91/TKF92 / MixDom / mixture-class models from the companion paper.
• bio-datasets/ (git submodule) — fetch scripts for Pfam / BAliBase / OxBench (no bundled data; corpora pulled at runtime).

Reproduction

See REPRODUCTION_MANIFEST.md for the complete recipe and pointers to released artefacts on this repo's GitHub Releases page.

Releases

Tag	Contents
code-2026-05-19	Source-code snapshot of this repo at the bioRxiv submission, packaged as a GitHub-generated tarball
results/K4-emwarm-top1000-2026-05-09	TKF-DP $K_c{=}4$ EM-warmup checkpoint (Pfam top-1000), backs Figs 3-5 and Table 1 row inf-PHMM-$K{=}4$
qprime-bali3pdbm-2026-05-16	Q' caches (per-pair posteriors) for all 8 methods compared in Tables 1+2, ~3.6 GB across 8 tarballs

The companion tkf-mixdom repo also has a release of trained checkpoints:

Repo	Tag	Contents
evoldoers/tkf-mixdom	mixdom-checkpoints-2026-05	MixDom-d3f1, TKF92-K=20, CherryML-C=20 NPZ ckpts (3 files, ~210 KB total)

License

Code: see LICENSE (or per-file headers). Paper and figures: CC-BY 4.0 (consistent with bioRxiv standard).