"How to perform commands in a terminal" matching MCP servers:

Enables genomic sequence analysis through the Evo 2 model, supporting DNA sequence scoring, embedding, generation, and variant effect prediction with multiple model checkpoints (7B, 40B, 1B parameters).

Enables variant annotation and effect prediction using the Ensembl VEP API, with support for batch and single queries.

An MCP server that interfaces with Gigwa for genotyping data import, analysis, and audit, enabling users to perform complex workflows through natural language commands.

Provides seamless access to the Protein Data Bank in Europe (PDBe) API and search capabilities, enabling AI clients to query protein structures, perform advanced searches, and retrieve structural biology data.

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.

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.

Connects PyMOL to Claude AI through the Model Context Protocol, allowing for conversational structural biology and molecular visualization through natural language commands.

An MCP server for the gget bioinformatics library that enables AI assistants to perform complex genomics queries, including gene sequence retrieval, BLAST alignments, and protein structure predictions.

A Model Context Protocol server that enables AI assistants to interact with LAMMPS for molecular dynamics simulations through natural language commands.

A specialized MCP server for Metal-Organic Framework research that provides tools for database searching, structural optimization, and energy calculations via ASE. It enables scientific workflows by allowing users to interact with MOF data and perform chemical simulations through a standard SSE interface.

Enables AI assistants to explore VEuPathDB WDK catalogs, searches, parameters, and gene data, and to perform gene lookups, expression summaries, step estimates, and download URL retrieval using VEuPathDB credentials.

Enables AI assistants to perform genomic variant analysis using OakVar, including running annotation pipelines, managing 200+ annotator modules, querying variant databases, and generating reports in various formats.

MCP server for RNA-seq downstream analysis, wrapping R scripts to generate plots and perform analyses like PCA, volcano, heatmap, enrichment, and WGCNA.

A terminal-based bioinformatics CLI chat tool that integrates Ensembl VEP, NCBI ClinVar, an MCP server layer, and OpenRouter's NVIDIA Nemotron 3 Ultra model to provide variant consequence and clinical significance lookups with clear summaries in a Rich-powered CLI.

Provides a natural language interface for single-cell RNA-Seq analysis using the decoupleR framework. It enables users to perform biological pathway inference, data clustering, and visualization through MCP-compatible AI clients.

Enables LLM agents to perform stateful genome-scale metabolic modeling with COBRApy through the Model Context Protocol, including loading models, knocking out genes, running flux balance analysis, and inspecting flux distributions.

BioOpenMCP enables users to run bioinformatics tools like FastQC, Cutadapt, and STAR with background execution and status checking. It integrates with Claude Desktop to perform quality control, trimming, alignment, and reporting via natural language.

Control PyMOL from Cursor via natural language. Enables describing molecular structures and styles in plain language to execute PyMOL commands through XML-RPC.

Enables LLMs and AI agents to query a biomedical knowledge graph stored in RedisGraph, with tools for concept search, synonym enrichment, and study variable discovery through semantic relationships.