Evolutionary MSA Data

This repository contains precomputed evolutionary sequence-alignment data in an archive format that is practical to host and download from the Hub. The original file paths are preserved inside the tar shard, while metadata.csv gives a searchable index of every file.

The dataset is meant for workflows that need ready-to-use MSA/cache files without rebuilding them from sequence databases.

Contents

Component	Files	Size
msa_cache/	134,898	19.37 GiB
mmseqs30/	4	82.32 MiB
root files	4	41.99 MiB

File types:

Type	Files	Size
.npz	134,898	19.37 GiB
.fasta	3	80.71 MiB
.parquet	1	34.33 MiB
.json	1	7.65 MiB
.tsv	1	1.61 MiB
.sh	1	806 B
.md	1	543 B

Packaging:

Item	Value
Indexed files	134,906
Original payload	19.49 GiB
Tar shards	1
Split large-file parts	0
Archive size	19.72 GiB
Metadata generated	2026-05-25T06:39:53Z

Layout

README.md
_MANIFEST.json
metadata.csv
shards.csv
parts.csv
shards/
  shard-00000.tar

Most users only need metadata.csv and shards/shard-00000.tar. The metadata table is configured as the default Dataset Viewer table.

Metadata

metadata.csv has one row per original file.

Column	Meaning
path	Original relative path.
storage_type	tar for files stored inside a tar shard; parts for oversized files split into byte parts.
shard_path	Tar shard containing the file.
member_path	Path of the file inside the tar shard.
parts_count	Number of split parts, if any.
part_paths	Semicolon-separated part paths, if any.
top_level, directory, filename, extension	Path fields for filtering.
size_bytes, size_human, modified_utc	Size and timestamp captured during packaging.

shards.csv lists archive shards. parts.csv is present for consistency with the archive format; this upload does not currently require split parts.

Python API Examples

Install recent Hugging Face clients in your environment:

# pip install -U huggingface_hub datasets

Set the repo id once:

repo_id = "LiteFold/Evolutionary"

Browse Files

from datasets import load_dataset

files = load_dataset(repo_id, "files", split="train")
print(files)
print(files[0])

For streaming access to the index:

from datasets import load_dataset

files = load_dataset(repo_id, "files", split="train", streaming=True)
for row in files:
    if row["extension"] == ".npz":
        print(row["path"], row["size_human"], row["shard_path"])
        break

Extract One MSA Cache File

This downloads the shard containing the selected file, then extracts only that member.

from pathlib import Path
import tarfile

from datasets import load_dataset
from huggingface_hub import hf_hub_download

repo_id = "LiteFold/Evolutionary"
out_dir = Path("./evolutionary")

files = load_dataset(repo_id, "files", split="train", streaming=True)
row = next(item for item in files if item["extension"] == ".npz")

shard = hf_hub_download(
    repo_id=repo_id,
    repo_type="dataset",
    filename=row["shard_path"],
)

with tarfile.open(shard) as archive:
    archive.extract(row["member_path"], path=out_dir)

print(out_dir / row["path"])

Restore The Full Tree

This downloads the repository snapshot and extracts all tar shards into a local directory.

from pathlib import Path
import csv
import tarfile

from huggingface_hub import snapshot_download

repo_id = "LiteFold/Evolutionary"
snapshot = Path(snapshot_download(repo_id=repo_id, repo_type="dataset"))
out_dir = Path("./evolutionary")
out_dir.mkdir(parents=True, exist_ok=True)

for shard in sorted((snapshot / "shards").glob("*.tar")):
    with tarfile.open(shard) as archive:
        archive.extractall(out_dir)

with (snapshot / "metadata.csv").open(newline="") as handle:
    for row in csv.DictReader(handle):
        if row["storage_type"] != "parts":
            continue
        target = out_dir / row["path"]
        target.parent.mkdir(parents=True, exist_ok=True)
        with target.open("wb") as dst:
            for part_path in row["part_paths"].split(";"):
                with (snapshot / part_path).open("rb") as src:
                    while chunk := src.read(8 * 1024 * 1024):
                        dst.write(chunk)

print(out_dir)

Notes

• The archive is uncompressed so individual files can be extracted directly from the tar shard.
• The file paths are kept as they appeared in the source data directory.
• Use metadata.csv as the source of truth for locating files inside shards.