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

pyfamsa

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

pyopal

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

mappy

A versatile pairwise aligner for genomic and spliced nucleotide sequences

bistring

Bidirectionally transformed strings

pymsaviz

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

kalign-python

A fast multiple sequence alignment program.

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

catnip-seq

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

plastburstalign

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

samsum

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

uta-align

C-based sequence alignment for Python

goombay

Python implementation of several local, global, and multiple sequence alignment algorithms intended to calculate distance, show alignment, and display the underlying matrices.

trviz

A python library for decomposing and visualizing tandem repeat sequences

polya

Automatically Adjudicate Any And All Arbitrary Annotations, Astutely Adjoin Abutting Alignments, And Also Amputate Anything Amiss (AAAAAAAAAAAAAAAA)

filtersam

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

sigalign

A Similarity-Guided Alignment Algorithm

pymsa

Scoring Multiple Sequence Alignments with Python

plotnineseqsuite

A Python package for visualizing sequence data using ggplot2 style

pairwise-sequence-alignment

Global and local pairwise alignments between nucleotide/protein sequences.

minimappers2

Rust bindings to minimap2 library