Stars
A minimalist tree plotting library using toyplot graphs
Extracted system prompts from ChatGPT (GPT-5.5 Thinking), Claude (Opus 4.7, Opus 4.6, Sonnet 4.6, Claude Code), Gemini (3.1 Pro, 3 Flash, Gemini CLI), Grok (4.3 beta), Perplexity, and more. Updated…
mtGrasp: de novo reference-grade mitochondrial genome assembly and standardization
Eukaryotic Genome Annotation Pipeline-External caller scripts and documentation
Organelle Genome Assembly Toolkit (Chloroplast/Mitocondrial/ITS)
A tool for discovering transposable elements and describing patterns of genome evolution
htseq / htseq
Forked from simon-anders/htseqHTSeq is a Python library to facilitate processing and analysis of data from high-throughput sequencing (HTS) experiments.
HTSeq is a Python library to facilitate processing and analysis of data from high-throughput sequencing (HTS) experiments.
Logic for running AlphaFold3 on an HPC cluster
AlphaFold 3 inference pipeline.
Kodu is an autonomous coding agent that lives in your IDE. It is a VSCode extension that can help you build your dream project step by step by leveraging the latest technologies in automated coding…
Genome modeling and design across all domains of life
Biological foundation modeling from molecular to genome scale
Cluster amino acid distributions for empirical distribution mixture models
A tool for concatenating multiple fasta alignments for supermatrix phylogenetic analyses
This is a new repository for Wammel, the phylogenetic hypothesis comparison tool.
Scoutknife is a naïve, whole genome informed phylogenetic robusticity metric
JFFleming / BaCoCa
Forked from PatrickKueck/BaCoCaBaCoCa (Base Composition Calculator) is designed to perform multiple statistical analyses on multiple nucleotide and amino-acid sequence alignments. The results of the BaCoCa analyses can be used f…
BOSTIn is a new, user-friendly phylogenetic artifact identification package.
RCFV reader is a new software to quickly calculate normalised relative compositional frequency variability.
An R package to identify and classify duplicated genes from whole-genome protein sequence data
Improved Inference of Ortholog Groups using Hidden Markov Models
A tool for automated alignment trimming in large-scale phylogenetic analyses. Development version: 2.0
an ensemble usage of MAFFT-linsi --add on large datasets