Sequence Analysis Python Packages

biotite

A comprehensive library for computational molecular biology

pyhmmer

Cython bindings and Python interface to HMMER3.

lightmotif

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

sequenzo

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

anomaly-grid-py

Python bindings of a Rust library for anomaly detection in finite alphabets using variable-order Markov chains.

pymsaviz

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

kalign-python

A fast multiple sequence alignment program.

peptides

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

pxblat

PxBLAT: An Efficient and Ergonomic Python Binding Library for BLAT

pymemesuite

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

gfapy

Library for handling data in the GFA1 and GFA2 formats

py-cdhit

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

midsv

a Python module to translate SAM into MIDSV format.

geneblocks

Library to compare DNA sequences (diff, common blocks, etc.)

seqann

Python package for doing fast and accurate sequence annotation

gramep

GRAMEP - Genome vaRiation Analysis from the Maximum Entropy Principle

pyncbitk

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

pyncbitk-runtime

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

vfind

Simple variant finding from NGS data

smof

Explore and analyze biological sequence data

codepub

Algorithms for sequence construction

seqsearch

Sequence similarity searches (e.g. BLAST) made easy

string-kernels

Polynomial String Kernel and linear time String Kernel. Supports multithreading and is compatible with Scikit-Learn SVMs.

ilearnplus

iLearnPlus is the first machine-learning platform with both graphical- and web-based user interface that enables the construction of automated machine-learning pipelines for computational analysis and predictions using nucleic acid and protein sequences.