FunVIP 
FunVIP is now published please cite:
Seo CW, Yoo S, Cho Y, Kim JS, Steinegger M, Lim YW. FunVIP: Fungal Validation and Identification Pipeline based on phylogenetic analysis. J. Microbiol. 2025;63(4):e2411017. Link
Fungal Validation & Identification Pipeline
An automatic tree-based sequence identification and validation pipeline for fungal (or maybe other) species
- Automatic tree-based identification
- Works with multiple genetic marker
- Database sequence validation algorithm implemented
Bug reports are always welcomed
Tutorial
Documentation
- See Documentation for advanced usage !
- See the command-line parameter reference for every option, or run
FunVIP --help
Requirements
- Conda or Mamba environment
* See here for how to install conda environment
* Recently, Mamba is a lot faster than conda. See here to how to install mamba environment
Installation
Quick install (conda / mamba)
The external aligners and tree tools install via conda; FunVIP and its Python dependencies (including ete4) install via pip (which works on Linux/macOS).
conda env create -f environment.yml # or: mamba env create -f environment.yml
conda activate funvip
FunVIP --test terrei --email you@example.com
Or run everything in a container (no local install; handy on Windows/WSL):
docker build -t funvip .
docker run --rm -v "$PWD:/data" funvip --test terrei --email you@example.com --outdir /data/out
Usage
FunVIP --db {Your database file} --query {Your query file} --email {Your email} --gene {Your genes} --preset {fast or accurate}
Example
FunVIP --db Penicillium.xlsx --query Query.xlsx --email {Your email} --thread 8 --gene ITS BenA RPB2 CaM --preset fast
Quick check
Verify your installation on a bundled dataset (needs an e-mail for the GenBank accessions):
FunVIP --test terrei --email {Your email}
* See documentation for detailed usage
How to make database?
Results
Outputs are written to {outdir}/{runname}/:
-
{runname}.result.csv: Final identification result: how each query was assigned to the group and species level through tree-based identification -
{runname}.dataset.csv: Clustering result: which group (e.g. genus/section) each sequence was assigned to -
{runname}.report.txt: Run report with the options used and a per-step summary. Taxa ending with a number are paraphyletic and should be checked -
07_Tree/{runname}_{group}_{gene}.svg: Final collapsed tree (SVG), editable in vector-graphics programs or PowerPoint (ungroup) -
07_Tree/{runname}_{group}_{gene}_original.svg: Uncollapsed tree for inspection -
Example output tree of FunVIP
Scheduling
Beta release part 1 (2023 Feburary ~ As paper published, ver 0.3) Will be tested by our lab memebers to fix bugs and advance features- Beta release part 2 (As paper published ~ When pipeline gets stabled, ver 0.4) Will be tested by peer taxonomists
- Stable release (ver 1.0)
Running the tests
pytest runs the fast unit tests (no external tools needed). pytest -m integration runs the end-to-end terrei test (needs the external tools on PATH and FUNVIP_TEST_EMAIL set). See tests/README.md.
License
1 maintainer
Release files for FunVIP 1.0.0
For a detailed explanation of source distributions (sdists) and built distributions (wheels), please see the package formats documentation.
Source distribution (sdist)
| File | Size | Uploaded | |
|---|---|---|---|
| funvip-1.0.0.tar.gz | 66.6 MB | Details |
Built distribution (wheel)
| File | Interpreter | ABI | Platform | Reset |
|---|---|---|---|---|
| funvip-1.0.0-py3-none-any.whl | Python 3 | none | any | Details |
Total release size: 133.5 MB
Release files / funvip-1.0.0.tar.gz
| Download URL | funvip-1.0.0.tar.gz |
|---|---|
| Size | 66.6 MB |
| Tags | Source |
|
SHA-256 checksum How to use checksums |
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No |
| Uploaded via |
twine/6.2.0 CPython/3.12.13
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Release files / funvip-1.0.0-py3-none-any.whl
| Download URL | funvip-1.0.0-py3-none-any.whl |
|---|---|
| Size | 66.9 MB |
| Tags | Python 3 |
|
SHA-256 checksum How to use checksums |
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BLAKE2b-256 checksum How to use checksums |
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Uploaded using Trusted Publishing? What is trusted publishing? |
No |
| Uploaded via |
twine/6.2.0 CPython/3.12.13
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