An MCP (Model Context Protocol) server for simulating DNA and amino acid sequences using various evolutionary models and algorithms. This server
An MCP (Model Context Protocol) server for simulating DNA and amino acid sequences using various evolutionary models and algorithms. This server provides powerful
Once MCP Sequence Simulation is connected, these are the calls the assistant has available:
Statistics — All tools provide detailed statistics including: - Sequence composition analysis - Mutation counts and types - Evolutionary parameters - PhylogeneticCompare MCP servers by category, or browse hosted MCP servers if you prefer an endpoint over a local process.
Check the linked publisher documentation and your connected client's tool list. Names and availability can vary with the server version and account permissions.
| Tool | What it does |
|---|---|
| length | required): Sequence length |
| gcContent | optional): GC content ratio (0-1, default: 0.5) |
| count | optional): Number of sequences (default: 1) |
| model | optional): "random", "hydrophobic-bias", or "disorder-prone" |
| seed | optional): Random seed |
| outputFormat | optional): "fasta", "nexus", or "phylip" |
| composition | optional): Custom amino acid frequencies |
| referenceSequence | required): Reference DNA sequence to generate reads from |
| readLength | required): Length of each sequencing read (50-300 bp) |
| coverage | required): Target sequencing coverage depth (1-1000x) |
| readType | optional): "single-end" or "paired-end" (default: "single-end") |
| insertSize | optional): Mean insert size for paired-end reads (default: 300) |
| insertSizeStd | optional): Standard deviation of insert size (default: 50) |
| errorRate | optional): Base calling error rate 0-0.1 (default: 0.01) |
| qualityModel | optional): "illumina", "454", "ion-torrent", or "pacbio" (default: "illumina") |
| mutationRate | optional): Mutation rate per branch length (default: 0.1) |
| sequence | required): Starting sequence |
| sequenceType | required): "dna" or "protein" |
| substitutionRate | optional): Substitution rate (default: 0.01) |
| insertionRate | optional): Insertion rate (default: 0.001) |
| deletionRate | optional): Deletion rate (default: 0.001) |
| transitionBias | optional): Transition vs transversion bias for DNA (default: 2.0) |
| iterations | optional): Number of mutation rounds (default: 1) |
| generations | required): Number of generations |
| populationSize | required): Population size |
| selectionPressure | optional): Selection strength (0-1) |
| fitnessFunction | optional): "gc-content", "length", "hydrophobic", or "custom" |
| targetValue | optional): Target value for fitness function |
| trackLineages | optional): Track individual lineages |
| rootSequence | required): Ancestral sequence |
| treeStructure | optional): Newick format tree or "random" |
| numTaxa | optional): Number of taxa for random tree (default: 5) |
| branchLengthVariation | optional): Branch length variation (default: 0.2) |
| molecularClock | optional): Use molecular clock (default: true) |
| substitutionModel | optional): "JC69", "K80", "HKY85", or "GTR" |
{
"mcpServers": {
"sequence-simulation": {
"command": "node",
"args": [
"dist/server.js"
],
"cwd": "/path/to/mcp-sequence-simulation"
}
}
}From the project documentation. Replace placeholders and example paths before connecting.
Read, search and edit files inside allowed directories with the Model Context Protocol reference Filesystem server.
Retrieve version-aware library documentation and code examples with Context7 MCP, using resolve-library-id and query-docs.
Use Microsoft’s Playwright MCP server to navigate pages, inspect accessibility snapshots, fill forms and capture browser screenshots.
Connect GitHub MCP to repositories, issues and pull requests with GitHub’s hosted service or a locally run server.
Use the Supabase MCP server to inspect database schemas, query project data and retrieve docs through a project-scoped connection.
Search Linear issues and projects, inspect work context and manage updates through Linear’s hosted MCP server with OAuth.