Software

DNALLM-Suite

A unified toolkit for fine-tuning and inference with DNA Language Models. Provides CLI, Web UI, and MCP (Model Context Protocol) support for seamless LLM integration. Features include fine-tuning pipelines, in-silico mutagenesis analysis, and support for multiple model architectures.

PDLLMs — Plant DNA Large Language Models

A group of tailored DNA large language models for analyzing plant genomes. Published in Molecular Plant 2025.

Citation: Liu GQ, Chen L, Wu YC, Han YS, Bao Y, Zhang T. PDLLMs: A group of tailored DNA large language models for analyzing plant genomes. Mol Plant. 2025;18(2):175-178.

dnallmmark

Benchmarking framework for DNA Large Language Models. Standardized evaluation metrics and datasets for comparing DNA LLM architectures.

MambaForSequenceClassification

HuggingFace integration for Mamba state-space models applied to DNA sequence classification. Enables efficient training for genomic sequences.

CrisprStitch

A fast, user-friendly tool to evaluate the efficiency of CRISPR-Cas editing systems. Available as a web application and desktop app. Performs all calculations locally on the user's computer without uploading data to remote servers.

Citation: Han YS, Liu GQ, Wu YC, Bao Y, Zhang Y, Zhang T. CrisprStitch: Fast evaluation of the efficiency of CRISPR editing systems. Plant Commun. 2024;5(3):100783.

Chorus2

A software pipeline to select genome-scale oligonucleotide-based probes for fluorescence in situ hybridization (Oligo-FISH). Highly effective at removing repetitive elements and selecting single-copy oligos. Supports probe design for species with or without assembled genomes.

Citation: Zhang T, Liu G, Zhao H, Braz GT, Jiang J. Chorus2: design of genome-scale oligonucleotide-based probes for fluorescence in situ hybridization. Plant Biotechnol J. 2021;19(10):1967-1978.

rustkmer

High-performance k-mer counting and analysis tool written in Rust for efficient processing of large genomic datasets.

SIF — Semantic Intelligence Framework

Semantic Intelligence Framework — a document semantic intelligence retrieval system. SIF provides collection management, hybrid search (BM25 + vector embeddings), and MCP server integration for AI-assisted document retrieval. Supports multiple embedding models including Sentence Transformers, GGUF, OpenAI-compatible APIs, and ModelScope Hub.