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.

pyfamsa

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

kalign-python

A fast multiple sequence alignment program.

mappy

A versatile pairwise aligner for genomic and spliced nucleotide sequences

cogent3

Comparative Genomics Toolkit 3

pymsaviz

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

sequence-align

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

bistring

Bidirectionally transformed strings

pyopal

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

stride-align

SIMD-accelerated fuzzy string matching, sequence alignment (Smith-Waterman / Needleman-Wunsch), edit distance (Levenshtein / OSA / Indel / Jaro-Winkler), phonetic encoders (Soundex / Metaphone / NYSIIS / Caverphone), and Dynamic Time Warping — x86 / ARM / LoongArch / POWER kernels with first-class CJK.

ont-mappy

A versatile pairwise aligner for genomic and spliced nucleotide sequences

uta-align

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

trviz

A python library for decomposing and visualizing tandem repeat sequences

plastburstalign

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

physquirrel

Squirrel: a Python package for reconstructing level-1 phylogenetic networks from sequence alignments or four-leaved networks

samsum

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

goombay

Python implementation of several sequence alignment algorithms such as Waterman-Smith-Beyer, Gotoh, and Needleman-Wunsch intended to calculate distance, show alignment, and display the underlying matrices.

catnip-seq

Explore nucleotide divergence and sequence resolution across user-defined categories.

filtersam

Tools to filter SAM/BAM files by percent identity and percent of matched sequence

bioforge

High-performance bioinformatics engine for edge computing. 5-bit encoding, vectorised NW alignment, 6-frame translation. NumPy + C backend. No Biopython.

filtersam-tools

Tools to filter SAM/BAM files by percent identity and percent of matched sequence

minibwa

Python bindings for minibwa

pymsa

Scoring multiple sequence alignments with Python