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Sequence Alignment Python Packages

Python packages with the GitHub topic sequence-alignment. Sorted by relevance, with stars and monthly downloads.
biopython
biopython

Official git repository for Biopython (originally converted from CVS)

8.9M 5K 2K
Martinsos
edlib

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

203K 593 171
cogent3
cogent3

Comparative Genomics Toolkit 3

23K 135 67
microsoft
bistring

Bidirectionally transformed strings

15K 368 15
lh3
mappy

A versatile pairwise aligner for genomic and spliced nucleotide sequences

15K 2K 461
althonos
pyfamsa

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

10K 41 4
TimoLassmann
kalign-python

A fast multiple sequence alignment program.

8K 155 34
moshi4
pymsaviz

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

8K 192 23
althonos
pyopal

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

7K 10 1
kensho-technologies
sequence-align

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

5K 75 3
lh3
ont-mappy

A versatile pairwise aligner for genomic and spliced nucleotide sequences

2K 2K 461
michaelgruenstaeudl
plastburstalign

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

2K 1 0
avitai
diffbio

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

1K 1 0
CIBIO-BU
catnip-seq

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

1K 0 0
biocommons
uta-align

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

999 6 6
Jong-hun-Park
trviz

A python library for decomposing and visualizing tandem repeat sequences

808 11 2
hallamlab
samsum

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

733 7 3
nholtgrefe
physquirrel

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

684 1 1
robaina
filtersam

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

394 6 0
lignum-vitae
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.

376 21 3
benhid
pymsa

Scoring Multiple Sequence Alignments with Python

303 23 10
jguhlin
minimappers2

Rust bindings to minimap2 library

293 111 21
baku4
sigalign

A Similarity-Guided Alignment Algorithm

289 30 4
TravisWheelerLab
polya

PolyA is a sequence annotation adjudicator.

266 8 2
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