Stars
a set of SKILLS.md for doing bioinformatics with agents like claude code
an interactive viewer for populations of bacterial genomes linked by a phylogeny
An agentic skills framework & software development methodology that works.
🤖 A production-grade framework for building AI-powered applications in R.
Nuitka is a Python compiler written in Python. It's fully compatible with Python 2.6, 2.7, 3.4-3.13. You feed it your Python app, it does a lot of clever things, and spits out an executable or exte…
A tool for automated alignment trimming in large-scale phylogenetic analyses. Development version: 2.0
Python package for building, comparing, annotating, manipulating and visualising trees. It provides a comprehensive API and a collection of command line tools, including utilities to work with the …
Simple phylogenetic tree visualization python package for phylogenetic analysis
Cython bindings and Python interface to MUSCLE v5, a highly efficient and accurate multiple sequence alignment software.
MSA(Multiple Sequence Alignment) visualization python package for sequence analysis
A Python library for the textbook Algorithms, 4th edition
scikit-bio: a community-driven Python library for bioinformatics, providing versatile data structures, algorithms and educational resources.
ML course materials for bioinformatics students following the Basic Machine Learning for Bioinformatics course at Utrecht University. Course created and taught by Dieter Stoker.
discovr package for R to accompany Discovering Statistics Using R and RStudio
Discovery of conserved gene clusters in multiple genomes
This project is dedicated to collecting high-quality macOS software and organizing them systematically by different categories for easy search and use.
拙著『「アルゴリズム×数学」が基礎からしっかり身につく本』（2021/12/25 発売）の GitHub ページです。演習問題の解答や、C++ 以外のソースコードなどが掲載されています。ぜひご活用ください。
Efficient phylogenomic software by maximum likelihood
Course materials for NAU's BIO 682 (Quantitative Biology), Spring semester 2025.
Foldseek enables fast and sensitive comparisons of large structure sets.
Code samples from the "Python Cookbook, 3rd Edition", published by O'Reilly & Associates, May, 2013.
Example code for Fluent Python, 2nd edition (O'Reilly 2022)
Code for the book Grokking Algorithms (https://www.amazon.com/dp/1633438538)