Evo2
Score, embed, and generate DNA sequences with Evo 2, a long-context genomic foundation...
Install
npx skills add aipoch/open-science --skill evo2 -g -a claude-code -y- Repository
- aipoch/open-science5.4k
- Category
- AI and agents
- Updated
- 3d ago
- License
- Apache-2.0
- Context cost
- Lightabout 1,130 tokens
- Runs scripts
- No, instructions only
What it does
Score, embed, and generate DNA sequences with Evo 2, a long-context genomic foundation model. Use this skill when: (1) Computing per-nucleotide or per-sequence likelihoods for variant effect scoring, (2) Embedding genomic windows for downstream classification, (3) Generating DNA conditioned on a prefix, (4) Scoring regulatory or coding regions across species.
Evo 2, DNA Language Model
Prerequisites
| Requirement | Minimum | Recommended |
|---|---|---|
| Python | 3.11 | 3.12 (<3.13) |
| CUDA | 12.1+ | 12.4+ |
| GPU VRAM | 24 GB (7B bf16) | 80 GB (40B) |
| RAM | 32 GB | 128 GB |
How to run
Installation
pip install evo2
# Weights pulled from Hugging Face on first model load.
Loading and scoring
from evo2 import Evo2
model = Evo2("evo2_7b") # or "evo2_40b", see model table
seqs = ["ATCG" * 50, "GGGCTTAA" * 25]
ll = model.score_sequences(seqs) # → list[float], mean per-token log-likelihood
print(ll)
Generation
out = model.generate(
prompt_seqs=["ATGAAAGCT"],
n_tokens=256,
temperature=0.7,
)
print(out.sequences[0])
Models
| Name | Params | Context | VRAM (bf16) | Notes |
|---|---|---|---|---|
evo2_7b | 7 B | 1 M nt | ~22 GB | Default; fits on a single 24 GB+ GPU |
evo2_40b | 40 B | 1 M nt | ~78 GB | H100 80 GB or multi-GPU |
evo2_1b_base | 1 B | 8 K nt | ~6 GB | FP8 path requires sm_89+ (H100) |
Output format
score_sequences returns a list[float] (or np.ndarray) of mean log-likelihoods,
one per input sequence. More negative ⇒ less likely under the model. For variant
effect, compute Δll = ll_alt - ll_ref over a fixed window.
generate returns a GenerationOutput with .sequences (list[str]), .logits
(list[Tensor]), and .logprobs_mean (list[float]), always populated, no flag required.
Decision tree
Need a DNA model?
│
├─ Per-base/per-sequence likelihood, generation → Evo 2 ✓
├─ Predict experimental tracks (expression, accessibility) → borzoi
└─ Protein, not DNA → fair-esm2 / esmfold2
