Installation¶

Prerequisites¶

AlleleFlux requires Python 3.7+ and depends on standard bioinformatics packages (pandas, numpy, scipy, biopython, pysam, rpy2, etc.). All dependencies are managed automatically during installation.

Using Conda or Mamba (Recommended)¶

You can use either conda or mamba (both are fine). AlleleFlux is available on conda-forge and Bioconda:

# Install with conda (or mamba)
conda install -c conda-forge -c bioconda alleleflux

# Activate the environment
conda activate alleleflux

From Source¶

For development or if you prefer installing from source:

git clone https://github.com/MoellerLabPU/AlleleFlux.git
cd AlleleFlux
pip install -e .

This installs AlleleFlux in editable mode with all command-line tools available.

Verify Installation¶

Confirm AlleleFlux is installed correctly:

alleleflux --help
alleleflux-profile --help

You should see help text describing available commands and options.

Available CLI Tools¶

AlleleFlux provides 30+ command-line tools organized by function:

Analysis: alleleflux-profile, alleleflux-allele-freq, alleleflux-scores, alleleflux-outliers, alleleflux-dnds
Preprocessing: alleleflux-qc, alleleflux-eligibility, alleleflux-metadata
Statistics: alleleflux-lmm, alleleflux-cmh, alleleflux-two-sample-paired, alleleflux-single-sample
Visualization: alleleflux-prepare-metadata, alleleflux-terminal-nucleotide, alleleflux-track-alleles, alleleflux-plot-trajectories
Utilities: alleleflux-create-mag-mapping, alleleflux-add-bam-path

For a complete reference, see CLI Reference.

Next Steps¶

Proceed to Quickstart to run your first analysis, or read the Overview for a conceptual introduction.