flumut 0.6.5

A tool to search for molecular markers with potential impact on the biological characteristics of Influenza A viruses of the A(H5N1) subtype.

FluMut is an open-source tool designed to search for molecular markers with potential impact on the biological characteristics of Influenza A viruses of the A(H5N1) subtype, starting from complete or partial nucleotide genome sequences.

For the complete documentation please visit FluMut site.

Installation

FluMut-GUI

FluMut-GUI is the graphical interface of FluMut, easy to use and easy to install. If you need the CLI version, check FluMut installation. Download the compiled version for your OS, double click on it and follow instructions to install FluMutGUI:

• Windows
• MacOS
• Linux

FluMut

FluMut is a CLI tool, if you prefer a graphical interface see FluMut-GUI installation.

Pip

FluMut is available on PyPI. Before installing FluMut via Pip you need:

• Python
• Pip (often packed with Python)

Then, you can install FluMut with this simple command:

pip install flumut

Bioconda

FluMut is also available on Bioconda. You can install using Conda or Mamba.

• Mamba (recommended)

mamba install -c bioconda flumut

• Conda

conda install -c bioconda flumut

Usage

Input

FluMut can analyze multiple A(H5N1) Influenza virus sequences simultaneously. It can handle partial and complete genome sequences of multiple samples. You must provide a single file containing all the nucleotide sequences in FASTA format. Sequences must adhere to the IUPAC code.

FluMut relies on the FASTA header to assign the sequence to a specific segment and sample. For this reason, the header must contain both a sample ID (consistent among sequences of the same sample) and one of the following segment names: PB2, PB1, PA, HA, NP, NA, MP, NS.

An example of input file can be downloaded here.

Basic usage

You can get the output file in an Excel format (user-friendly) running:

flumut -x excel_output.xlsm your_fasta.fa

If you prefer the text outputs (machine-readable format) run:

flumut -m markers_output.tsv -M mutations_output.tsv -l literature_output.tsv your_fasta.fa

Update database

You should always use the latest version of our database and you can do it just by running this command:

flumut --update

Outputs

FluMut can produce an Excel output or text outputs:

• Excel
• Text outputs

By default FluMut reports only markers where all mutations are found. You can report all markers where at least one mutation is found using option -r/--relaxed.

Excel

This is the most user-friendly and complete output. You can obtain this output using the -x/--excel-output option. Find out more here.

IMPORTANT: To enable the navigation feature the exstension of the Excel file must be .xlsm. If you don't care about navigation, you can use .xlsx exstension. Other exstensions lead to unreadable files.

Text outputs

You can obtain 3 different text outputs:

Option	Output	Desctription
-m/--markers-output	Markers output	List of detected markers
-M/--mutations-output	Mutations output	List of amino acids present in the positions of mutations of interest for each sample
-l/--literature-output	Literature output	List of all papers present in the database

Cite FluMut

If you use FluMut, please cite:

Giussani, E., Sartori, A. et al. (2025). FluMut: a tool for mutation surveillance in highly pathogenic H5N1 genomes. Virus Evolution, 10.1093/ve/veaf011.

License

FluMut is licensed under the GNU Affero v3 license (see LICENSE).

Fundings

This work was partially supported by the FLU-SWITCH Era-Net ICRAD (grant agreement No. 862605), by EU funding under the NextGeneration EU-MUR PNRR Extended Partnership initiative on Emerging Infectious Diseases (Project No. PE00000007, INF-ACT), and by KAPPA-FLU HORIZON-CL6-2022-FARM2FORK-02-03 (grant agreement No. 101084171).

Views and opinions expressed are however those of the author(s) only and do not necessarily reflect those of the European Union or the European Health and Digital Executive Agency (HEDEA). Neither the European Union nor the granting authority can be held responsible for them