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.

cogent3

Comparative Genomics Toolkit 3

bistring

Bidirectionally transformed strings

mappy

A versatile pairwise aligner for genomic and spliced nucleotide sequences

pyfamsa

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

kalign-python

A fast multiple sequence alignment program.

pymsaviz

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

pyopal

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

sequence-align

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

ont-mappy

A versatile pairwise aligner for genomic and spliced nucleotide sequences

plastburstalign

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

diffbio

End-to-end differentiable bioinformatics pipelines built on JAX/Flax NNX

catnip-seq

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

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

samsum

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

physquirrel

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

filtersam

('Tools to filter sam o bam files by percent identity or percent of matched sequence',)

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.

pymsa

Scoring Multiple Sequence Alignments with Python

minimappers2

Rust bindings to minimap2 library

sigalign

A Similarity-Guided Alignment Algorithm

polya

PolyA is a sequence annotation adjudicator.