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.

pymsaviz

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

anomaly-grid-py

Deviation detection using variable-order Markov-chains in finite alphabet sequences

peptides

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

lightmotif

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

pyrsx

Rust RAD-seq marker analysis

midsv

a Python module to translate SAM into MIDSV format.

dotmatch

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

pymemesuite

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

pxblat

PxBLAT: An Efficient and Ergonomic Python Binding Library for BLAT

gfapy

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

geneblocks

:diamond_shape_with_a_dot_inside: Find common blocks and differences between DNA sequences

seqann

Sequence Annotation

codepub

Algorithms for sequence construction

py-cdhit

A Python package for CD-HIT, clustering protein or nucleotide sequences.

gramep

GRAMEP - Genome vaRiation Analysis from the Maximum Entropy Principle

vfind

Simple variant finding utilities for NGS data

smof

Explore and analyze biological sequence data

pyncbitk

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

flexidot

Highly customizable, ambiguity-aware dotplots for visual sequence analyses

pyncbitk-runtime

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