Bioinformatics Tool Python Packages

hbat

HBAT 2: A Python Package to analyse Hydrogen Bonds and Other Non-covalent Interactions in Macromolecular Structures

rosettapy

A Python utility for wrapping Rosetta command line tools.

bioat

bioat, a python package & command line toolkit for Bioinformatics and data science!

finaletoolkit

FinaleToolkit is a package and standalone program to extract fragmentation features of cell-free DNA from paired-end sequencing data.

hide-deconv

Repository for ECCB 2026 Poster Submission. Will be made available for reviewing after submission. For earlier access contact Dennis.k.volkl@uib.no

rnalysis

RNAlysis is an analysis software for RNA sequencing data. RNAlysis can help to filter, visualize, explore, analyze, and share your data.

tidytcells

Standardise TR/MH/IG data

squarna

RNA secondary structure prediction tool

easyfasta

A lightweight functional Python library for efficient FASTA file parsing and DNA sequence manipulation. No OOP bloat, data only data.

ampidentifier

Sequence-based identification of antimicrobial peptides using physicochemical feature engineering and a soft-voting ensemble of five classifiers

binette

A fast and accurate binning refinement tool to constructs high quality MAGs from the output of multiple binning tools.

biobase

A comprehensive package of biological constants, serving as a foundational resource for biology and bioinformatics, complemented by functions to streamline related tasks.

rosetta-finder

Searching for Rosetta Binaries.

pacs-q

PaCS-Q is a Python toolkit designed to assist with Parallel Cascade Selection simulations (PaCS) for studying protein structural transitions in MD and QM/MM MD level.

stitchr

Stitchr - a Python script to stitch together coding TCR nucleotide sequences from V, J, and CDR3 info

gps-mapping

Genetics-informed pathogenic spatial mapping

phigaro

Phigaro is a scalable command-line tool for predicting phages and prophages

geneview

Genomics data visualization in Python by using matplotlib.

genegrouper

CLI tool for finding gene clusters in many genomes and placing them in discrete groups based on gene content similarity.

gsmap

Integrating GWAS and spatial transcriptomics for spatially resolved mapping of cells associated with human complex traits.

viola-sv

Viola is a flexible and powerful python package designed specifically for analysis of genomic structural variant (SV) signatures.

codonu

An integrated package for codon usage analysis

evolharvester

parsing utility for transforming HyPhy (and eventually PAML) analysis insights into highly-ordered CSVs

pybiotk

生信常用工具合集，包括gtf/fastx/bam/bed格式文件的处理和转换，bam,bed注释工具，R绘图脚本等。