TyCHE documentation

Under construction

This site is still under construction. Be aware that some information may be missing or incorrect.

Welcome to TyCHE!

TyCHE is a Bayesian phylogenetics BEAST2 package that infers time trees of populations with distinct evolutionary rates. Mutation rates often vary dramatically by cell type, and TyCHE improves accuracy of trees for these heterogeneously evolving populations by simultaneously reconstructing ancestral cell types and inferring the time tree by linking those cell types to mutation rates for each branch.

TyCHE stands for Type-linked Clocks for Heterogenous Evolution, and is named in honor of the Greek goddess of chance in recognition of the stochastic nature of Bayesian analysis.

Contact

If you need help or have any questions, please contact the Hoehn Lab.

If you have discovered a bug or have a feature request, you can open an issue using the issue tracker.

Authors

Jessie Fielding

Sherry Wu

Hunter Melton

Kenneth Hoehn

Getting Started

We recommend starting with Build TyCHE Trees Using Dowser.

A BEAUti template for TyCHE is under development and will be made available soon.

Contents:

• About TyCHE
• Build TyCHE Trees Using Dowser
• API Reference

Citing

To cite the TyCHE package in publications, please use:

Fielding J, Wu S, Melton H, Du Plessis L, Fisk N, Hoehn K (2025). “TyCHE enables time-resolved lineage tracing of heterogeneously-evolving populations.” bioRxiv 2025.10.21.683591 doi:10.1101/2025.10.21.683591 https://doi.org/10.1101/2025.10.21.683591

License

AGPL-3