"Using Command Line with MCP (Master Control Program)" matching MCP servers:

Enables DNA sequence analysis and variant effect prediction using Evo2-7B via MCP tools, providing forward inference, likelihood scoring, and batch variant comparison through natural language.

Enables analysis of bulk RNA-seq data using natural language queries, executing R and Python in a Docker container with automatic sample anonymization and privacy controls.

A Model Context Protocol server that interfaces with Biomart databases, allowing models to discover biological datasets, explore attributes/filters, retrieve biological data, and translate between different biological identifiers.

An MCP server that provides tools for searching and fetching protein data from the UniProt database using the unipressed library.

MCP server for single-cell lineage tracing analysis, enabling conversational reconstruction, visualization, and heritability analysis of lineage trees using Cassiopeia, pycea, and treedata.

Connects 3D Slicer with AI assistants through the Model Context Protocol, enabling medical image processing and scene manipulation using natural language.

Provides an MCP interface to the ROBOT command-line tool for OWL ontology editing, enabling operations like merging, reasoning, and conversion via natural language.

Enables natural language control of UCSF ChimeraX for protein structure visualization, editing, and analysis through MCP clients.

Enables protein structure and sequence searches using FoldSeek, with support for multiple databases, automatic model downloads, and structured job management.

Allows to retrieve information about an AnnData object via MCP using the read_lazy function from anndata.

Enables AI assistants to perform NCBI BLAST sequence similarity searches through natural language, supporting nucleotide and protein searches, custom database creation, and multiple output formats.

Enables AI agents to search, filter, download files, and generate reports from the IGVF Data Portal using natural language commands.

An embedded MCP server for Cytoscape Desktop that lets AI agents load networks, set active views, and control the desktop application over HTTP.

Enables AI assistants to perform quality control analysis on high-throughput sequencing data using FastQC and MultiQC. It supports single-file and batch processing of FASTQ/FASTA files and generates comprehensive, interactive summary reports.

An MCP server that enables AI assistants to generate, score, and analyze DNA sequences using the evo2 genomic foundation model. It supports multiple execution modes including local GPU, SLURM clusters, and the Nvidia NIM cloud API for tasks like variant effect prediction and sequence embedding.

MCP server for interacting with Galaxy bioinformatics platform, enabling AI assistants to connect to Galaxy instances, search and execute tools, manage workflows, and access other features.

Enables AI agents to control RELION 5.x cryo-EM structure determination software through natural language, providing 23 tools for the complete single-particle analysis pipeline.

An MCP server for running local LLMs using llama-cpp-python, with built-in tools for generating drug-like molecule SMILES.

Enables AI assistants to perform DNA/RNA sequence alignment using BWA (Burrows-Wheeler Aligner), supporting both short and long read alignment to reference genomes with indexing, BWA-MEM, and BWA-backtrack algorithms.

Provides a natural language interface for scRNA-Seq analysis using the Scanpy library, supporting operations such as data preprocessing, clustering, and visualization. It enables AI agents and clients to perform complex single-cell transcriptomics workflows through the Model Context Protocol.