A Python library for simulating the evolution of species, genomes, sequences and traits

A tool for recovering synteny blocks from multiple alignment

A curated list of awesome Helix editor resources, plugins, themes, and tools.

Trees related to VGP

Mobile (Genetic) Element finder using DIVergence and ALignment. A parallelized sequence alignment tool for detecting Mobile Genetic Elements (MGEs) using BLAT and phylogenetic divergence analysis.

Flags phylogenetic anomalies across the genome using Expectation-Maximization and HMMs.

Fast and accurate tool for estimating genomic distances between genome-skims

Project documentation with Markdown.

Fast Whole-Genome Similarity (ANI) Estimation

Pinpoints the mutation favored by selection

[ICLR 2026 Gen2 Workshop Oral Spotlight] GPC: An expressive and tractable deep generative model for genetic variation data

Hierarchical Alignment Format

A minimalist tree plotting library using toyplot graphs

Reproducible code for McKenzie and Eaton waiting distance paper

Riemannian Adaptive Optimization Methods with pytorch optim

GFF and GTF file manipulation and interconversion

AI-powered code assistant for Vim. OpenAI and ChatGPT plugin for Vim and Neovim.

LLM inference in C/C++

An open-source AI coding agent that lives in your terminal.

Vim plugin for LLM-assisted code/text completion

Neovim plugin to generate text using LLMs with customizable prompts

✨ AI Coding, Vim Style

Claude vim plugin for AI pair programming - a hacker's gateway to LLMs

Task management for the Obsidian knowledge base.

Improved table navigation, formatting, and manipulation in Obsidian.md

A color theme for the tmux terminal multiplexer using Ethan Schoonover’s Solarized color scheme

Due to many requests I share my zsh configuration compilation.

Tmux Plugin Manager

Get up and running with Kimi-K2.6, GLM-5.2, MiniMax, DeepSeek, gpt-oss, Qwen, Gemma and other models.