Sequence Analysis Python Packages

biotite

A comprehensive library for computational molecular biology

pyhmmer

Cython bindings and Python interface to HMMER3.

sequenzo

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

anomaly-grid-py

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

kalign-python

A fast multiple sequence alignment program.

pymsaviz

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

peptides

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

lightmotif

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

pymemesuite

Cython bindings and Python interface to the MEME suite.

midsv

Python module to convert SAM to MIDSV format.

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

codepub

CodePUB

seqann

Sequence Annotation

geneblocks

:diamond_shape_with_a_dot_inside: Find common blocks and differences between DNA sequences

smof

Explore and analyze biological sequence data

py-cdhit

A Python interface for CD-HIT package.

pyncbitk

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

gramep

GRAMEP - Genome vaRiation Analysis from the Maximum Entropy Principle

vfind

Simple variant finding from NGS data

seqsearch

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

pyncbitk-runtime

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

string-kernels

Implementation of the Polynomial String Kernel and linear time String Kernel implementation. Compatible and ready for easy plug-in to Scikit-Learn's Support Vector Machines and supports multithreading.

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.