Sequence Analysis Python Packages

biotite

A comprehensive library for computational molecular biology

pyhmmer

Cython bindings and Python interface to HMMER3.

kalign-python

A fast multiple sequence alignment program.

sequenzo

A fast, scalable, and intuitive Python package in sequence analysis.

lightmotif

A lightweight platform-accelerated library for biological motif scanning using position weight matrices.

dotmatch

Fast exact short-DNA known-target assignment for CRISPR guides, barcodes, primers, panels, and whitelists.

pymsaviz

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

lzgraphs

Alignment-free graph models of TCR and BCR repertoires built from Lempel-Ziv and FlashBack string decompositions. Compute sequence generation probability (Pgen) and repertoire diversity, and generate new sequences. Python with a C core.

midsv

a Python module to translate SAM into MIDSV format.

peptides

Physicochemical properties, indices and descriptors for amino-acid sequences.

scrna-matrix

High-performance C++ genomics library and Python extension for fast omics processing, sequence analysis, and stream profiling.

pxblat

PxBLAT: An Efficient and Ergonomic Python Binding Library for BLAT

openomicsbench

Traceable omics benchmarks with multi-method matrices, regression gates, portable bundles and sequence tools.

pymemesuite

Cython bindings and Python interface to the MEME suite, a collection of tools for the analysis of sequence motifs.

pto-core

High-performance C++ genomics library and Python extension for fast omics processing, sequence analysis, and stream profiling.

pyrsx

Rust RAD-seq marker analysis

specimux

High-performance dual barcode and primer demultiplexer for MinION sequenced reads, optimized for fungal DNA barcoding.

gp3sequencespy

Transparent, reproducible sequence analysis in Python. Audit ordered categorical data, discover recurring structure, compare trajectories, model transitions and latent states, test group differences, and report every analytical choice.

geneblocks

:diamond_shape_with_a_dot_inside: Find common blocks and differences between DNA sequences

gfapy

Gfapy: a flexible and extensible software library for handling sequence graphs in Python

biosuite-ultra

Integrated pure-Python bioinformatics platform: 47 analysis modules, 105 plotting functions, molecular cloning with 169 restriction enzymes, and reproducible workflows through Python, CLI, GUI, and REST API.

pyncbitk-runtime

Cython bindings and Python interface to the NCBI C++ ToolKit (including BLAST+).

seqevi

Content-addressed, reusable protein sequence annotation evidence.

codepub

Algorithms for sequence construction