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Python and Biology

General Bioinformatics Frameworks

These libraries provide broad biological functionality (sequence analysis, file parsing, etc.):

  • Biopython - The de facto standard library for bioinformatics in Python. Tools for parsing FASTA/GenBank, working with sequences, BLAST, alignments, phylogenetics, etc.
  • Scikit-bio - Bioinformatics and computational biology toolkit built on NumPy. Focus on microbiome analysis, sequence data, diversity metrics, and statistics.
  • BioPandas - Extends pandas for structural biology data (PDB, mmCIF). Integrates molecular data frames with protein 3D structure parsing.

Genomics / Transcriptomics

Libraries for working with genome sequences, reads, and expression data:

  • pysam - Python interface to SAMtools and BCFtools. For reading/writing SAM/BAM/VCF files efficiently.
  • pybedtools - Python wrapper around BEDTools. For genome interval operations (overlaps, unions, intersections).
  • HTSeq - For analyzing high-throughput sequencing (RNA-Seq, etc.). Counts reads, annotates features, handles GFF/GTF formats.
  • anndata - Data structure for annotated data matrices (used in single-cell). Foundation for many single-cell analysis tools (e.g. scanpy).
  • scanpy - Analysis toolkit for single-cell RNA-seq data. Supports clustering, visualization, trajectory inference, etc.
  • pyranges - Fast genomic interval operations in pure Python. Like pybedtools, but implemented with pandas for speed. Better to use pyranges_1.
  • cyvcf2 - Fast VCF parser and query tool.

Proteomics and Structural Biology

Working with proteins, molecular dynamics, and structural data:

  • MDAnalysis - Analyze molecular dynamics trajectories. Supports many formats (GROMACS, AMBER, etc.).
  • ProDy - For protein structure and dynamics analysis.
  • PyMOL API - Python interface to PyMOL for visualizing 3D molecular structures.
  • biotite - Structural bioinformatics and sequence analysis; fast and modern.

Phylogenetics and Evolution

Tools for working with trees, evolutionary analysis, and alignments:

  • ETE Toolkit - Phylogenetic tree analysis, visualization, and manipulation.
  • DendroPy - For phylogenetic computing with trees and taxon data.
  • toytree - Lightweight and fast tree visualization and manipulation.

Systems Biology & Pathways

Libraries for metabolic models, pathways, and systems simulation:

  • COBRApy - Constraint-based modeling for metabolic networks.
  • Tellurium - Modeling and simulation of biochemical networks.
  • libSBML - Work with SBML (Systems Biology Markup Language).
  • PySCeS - Python Simulator for Cellular Systems.

Microbiome and Metagenomics

  • QIIME 2 API - Framework for microbiome analysis and reproducibility.
  • biom-format - Read/write BIOM tables (Biological Observation Matrix format).

Population Genetics

  • msprime - Efficient simulation of population genetic data.
  • tskit - Tree sequence toolkit for storing and analyzing genealogical data.

Cheminformatics

(Overlaps with computational chemistry, but widely used in drug design and molecular biology)

  • RDKit - Standard for cheminformatics: molecular fingerprints, descriptors, SMILES parsing.
  • Open Babel (Pybel) - Chemical toolbox for converting between molecular file formats.

More Python libraries used in biology

  • pyrosetta.distributed - The Python interface to Rosetta in cluster / distributed computing contexts.
  • pyrosetta.bindings - Bindings for Rosetta energy functions only - used almost nowhere outside protein design labs.

Genomics & Sequencing

  • dnaio - Fast FASTA/FASTQ reader/writer used under the hood by cutadapt.
  • cutadapt (Python API) - Adapter trimming library - most people use the CLI, but it has a Python API.
  • python-edlib - Ultra-fast library for edit distance / approximate sequence alignment (bindings for Edlib C library).
  • parasail-python - Bindings to the Parasail SIMD-accelerated pairwise alignment routines.
  • mappy - Python bindings to minimap2 for ultra-fast genome mapping.
  • pyfaidx - FASTA indexing and fast random access (like samtools faidx, but in Python).
  • screed - Indexed FASTA/FASTQ reader optimized for streaming very large datasets.
  • sourmash - Implements MinHash comparisons for genomic sketching, metagenomics, and large-scale sequence similarity.
  • khmer - K-mer counting, compression, and probabilistic data structures for huge genomes.
  • xopen - Handles compressed files (bgzip, gz) more efficiently than standard Python readers; used in many seq tools.

Neuroscience & Neurobiology

  • neo - Data model library for electrophysiology experiment formats.
  • elephant - Statistical analysis for spiking neural data (built on Neo).
  • PyNWB / HDMF - Work with the Neurodata Without Borders (NWB) data standard.
  • brian2 - Spiking neural network simulator used in theoretical neuroscience.
  • pyabf - Reading Axon Binary File (ABF) electrophysiology files.
  • pylake - Control and analysis for optical tweezer experiments (LUMICKS instruments)

Structural biology / Chemical biology

  • PyEMMA - Markov state modeling for protein conformational dynamics.
  • MSMBuilder - Machine learning library for analyzing molecular dynamics trajectories.
  • MDtraj - Specialized molecular dynamics trajectory analysis toolkit.
  • molecool - Small library for manipulating molecular structures intended for teaching but used in niche workflows.
  • pdbfixer - Automatically fix missing atoms/residues in PDB files - used before MD simulations.

Systems biology & Modelling

  • cobra-me - For modeling macromolecular expression models ("ME models") - very specialized.
  • PEtab / pyPESTO - Parameter estimation for systems biology models.
  • sbnet (Systems Biology Notebook) - Experimental toolkit for rule-based modeling workflows.
  • Bionetgen Python API - Bindings for BioNetGen rule-based modeling platform.

Microbiology / Metagenomics

  • anvi'o (Python API) - High-dimensional microbial & metagenomic analysis framework. CLI is famous; the Python API is lesser known.
  • genomeview - Python library for visualizing aligned reads and annotations directly from BAM/VCF/FASTA.
  • anvi-snakemake / anvio-structure - Extensions for structural metagenomics
  • mmgenome2 (Python parts) - Toolkit for metagenome binning; consists partly of Python libraries.

Population genetics

  • allel (scikit-allel) - Analysis of large-scale population genetics data (VCF, Zarr-based).
  • fwdpy11 - Forward-time evolutionary simulations (selection, demography).
  • moments - Demographic inference from site-frequency spectra.
  • dadi - Another demographic inference tool (Diffusion Approximations for Demographic Inference).

Proteomics

  • pyteomics - Parsing MS/MS mass spectrometry formats (mzML, mzXML, MGF).
  • alphapept - End-to-end proteomics pipeline with a Python engine.
  • ms_deisotope - Deisotoping + charge state deconvolution for mass spec signals.
  • GlyPy - Glycoinformatics library - glycan structures & mass spec data.

Phylogenetics

  • biopython-phylip - Sxtensions for interacting with PHYLIP tools.
  • augur (Nextstrain) - Python API for phylogenetic pipelines (used heavily in genomic epidemiology).
  • phylopandas - Integrates phylogenetic sequences & metadata into a pandas-like API.
  • pastml - Phylogenetic ancestral state reconstruction in Python.

Microscopy / Image analysis

  • aicsimageio - Read microscopy data from proprietary formats (CZI, OME-TIFF, etc.).
  • czifile - Read Zeiss CZI microscopy images.
  • cellpose (Python API) - Deep learning-based cell segmentation.
  • napari (with bioimage-specific plugins) - Interactive viewer - not strictly a “biology" library, but most of its ecosystem is microscopy-oriented.

Animal tracking / Behavioral biology

  • dlc (DeepLabCut) - Pose estimation software used for tracking animal behavior.
  • SLEAP - Multi-animal pose tracking using deep learning.

Plant biology

  • PlantCV - Computer vision toolkit for plant phenotyping.

Bioinformatics adjacent / "Strange but real"

  • skmer - Genome distance estimation without assembly using spectral k-mer methods.
  • phylter - Detect suspicious sequences in phylogenetic datasets (contaminants and outliers).
  • pyslim - Manipulate tree sequences produced by SLiM evolutionary simulations.
  • pp-sketchlib - MinHash sketches for petabase-scale genomics (used by BIGSI databases).
  • pyswift - Machine-learning-based annotation for Schizosaccharomyces pombe datasets