Sequence Alignment Python Packages

biopython

Official git repository for Biopython (originally converted from CVS)

edlib

Lightweight, super fast C/C++ (& Python) library for sequence alignment using edit (Levenshtein) distance.

scikit-bio

scikit-bio: a community-driven Python library for bioinformatics, providing versatile data structures, algorithms and educational resources.

pyfamsa

Cython bindings and Python interface to FAMSA, an algorithm for ultra-scale multiple sequence alignments.

mappy

A versatile pairwise aligner for genomic and spliced nucleotide sequences

sequence-align

Efficient implementations of Needleman-Wunsch and other sequence alignment algorithms written in Rust with Python bindings via PyO3.

kalign-python

A fast multiple sequence alignment program.

msasim

Backend C++ code for the Sailfish MSA simulation library using the Pybind11 framework

cogent3

Comparative Genomics Toolkit 3

pyopal

Cython bindings and Python interface to Opal, a SIMD-accelerated database search aligner.

pymsaviz

MSA(Multiple Sequence Alignment) visualization python package for sequence analysis

diffbio

End-to-end differentiable bioinformatics for JAX/Flax NNX: soft Smith-Waterman alignment, read mapping and assembly, variant calling, RNA-seq, single-cell, epigenomics, CRISPR, metabolomics, multi-omics, protein and RNA structure, molecular dynamics and drug-discovery operators composed into trainable pipelines on the Avitai stack.

uta-align

C-based Needleman-Wunsch and Smith-Waterman alignment algorithms with a Python interface.

bioforge

High-performance bioinformatics engine for edge computing. 5-bit encoding, vectorised alignment, DNA→protein translation, and a minimap2-style genome mapper — whole pipeline in C behind a thin NumPy cover. pip install bioforge.

flashalign

A fast aligner for long DNA and RNA reads.

myers-batch

Batched infix edit distance: bit-parallel Myers for aarch64 NEON and x86-64 AVX2, 7.5-10x faster than edlib single-threaded on the reference machine

stride-align

High-performance Python/C++ string and sequence alignment: Smith-Waterman, Needleman-Wunsch, Levenshtein, Damerau-Levenshtein, Jaro, and batch fuzzy matching.

mgnifam

Build protein families from sequence clusters by iterative HMM search over very large databases — streaming, deterministic, pyHMMER-based.

ont-mappy

A versatile pairwise aligner for genomic and spliced nucleotide sequences

alignair

Deep-learning V(D)J aligner for BCR and TCR sequences. A single model predicts V/D/J allele calls, segment boundaries and the junction, with AIRR-format output. Published in Nucleic Acids Research (2025).

pymsa

Scoring multiple sequence alignments with Python

plastburstalign

A Python tool to extract and align genes, introns, and intergenic spacers across thousands of plastid genomes using associative arrays

orthoevol

An easy to use and comprehensive python package which aids in the analysis and visualization of orthologous genes. 🐵

samsum

A light-weight python package for summarizing sequence coverage from SAM and BAM files