| name | lucaphylo |
| description | LucaPhylo — alignment-free phylogenetic inference / placement via hyperbolic protein language models (ESM2 + hyperbolic geometry). Use when: (1) MSA-based trees fail on highly divergent proteins, (2) Exploring PLM phylogeny as a complement to IQ-TREE/PhyloPhlAn, (3) Following the LucaPhylo training or placement checkpoints. Upstream: https://github.com/NickShannn/LucaPhylo. Route via phylogenomics; do not replace GTDB-Tk for MAG taxonomy by default.
|
| license | MIT |
| category | analysis-tools |
| tags | ["LucaPhylo","PLM","phylogeny","hyperbolic","alignment-free","ESM2"] |
| upstream | https://github.com/NickShannn/LucaPhylo |
| stage | taxonomy |
LucaPhylo
Upstream: NickShannn/LucaPhylo ·
Checkpoints: https://huggingface.co/NickShan/LucaPhylo
Citation
Shan, Y. et al. Alignment-free phylogenetic inference via hyperbolic protein
language models. bioRxiv https://doi.org/10.64898/2026.05.26.723419 (2026).
See also docs/references.md.
Analytical thinking
Classical phylogenomics needs MSAs. LucaPhylo places unaligned proteins
using ESM2 embeddings adapted into hyperbolic space — aimed at highly divergent
sequences (training emphasis includes viral RdRP / polyprotein settings). Treat
as an AI phylogeny track next to iqtree / phylophlan, not as default MAG
taxonomy (gtdbtk).
| vs | Prefer LucaPhylo when |
|---|
iqtree / phylophlan | MSA unreliable or discarded divergent taxa |
homology-search | Goal is a tree/placement, not hit tables |
gtdbtk | Never as sole bacterial MAG taxonomy |
Pin checkpoint stage (1–4), backbone tree, and that results are computational
hypotheses. GPU recommended for training; inference benchmarks include CPU/GPU
profiles in upstream docs.
How to run
conda create -n lucaphylo python=3.10.16
conda activate lucaphylo
git clone https://github.com/NickShannn/LucaPhylo.git
cd LucaPhylo
pip install -r requirements.txt
Do not invent CLI flags — follow the repository scripts for the installed tag.
Decision tree
Phylogeny without reliable MSA?
├─ Yes, PLM/hyperbolic placement → lucaphylo
├─ Standard MAG/marker phylogenomics → phylophlan → iqtree
├─ Taxonomy placement only → gtdbtk
└─ Homology search only → homology-search
Related skills
phylogenomics · protein-language-model · esm · iqtree · phylophlan ·
metagenomics-llm · omg · gtdbtk · tool-selection
