MCP Sequence Simulation Server
Server Configuration
Describes the environment variables required to run the server.
| Name | Required | Description | Default |
|---|---|---|---|
No arguments | |||
Instructions
Guidance the server publishes about itself, which clients place ahead of the tool catalog so the model reads it before choosing anything.
This server publishes no instructions, or was last inspected before Glama recorded them.
Capabilities
Features and capabilities supported by this server
Protocol revision2025-11-25
| Capability | Details |
|---|---|
| tools | {} |
Tools
Functions exposed to the LLM to take actions
| Name | Description |
|---|---|
| generate_dna_sequenceC | Generate random DNA sequences with specified parameters |
| generate_protein_sequenceB | Generate random protein sequences with specified parameters |
| mutate_sequenceC | Apply mutations to DNA or protein sequences |
| evolve_sequenceC | Simulate evolution of sequences over multiple generations |
| simulate_phylogenyC | Simulate phylogenetic tree and sequence evolution |
| simulate_fastq_fileB | Simulate FASTQ sequencing reads with realistic quality scores and error models based on NEAT methodology. Implementation inspired by: Stephens et al. (2016) 'Simulating Next-Generation Sequencing Datasets from Empirical Mutation and Sequencing Models.' PLOS ONE 11(11): e0167047. https://doi.org/10.1371/journal.pone.0167047 |
Prompts
Interactive templates invoked by user choice
| Name | Description |
|---|---|
No prompts | |
Resources
Contextual data attached and managed by the client
| Name | Description |
|---|---|
No resources | |
TDQS
Scored across 6 tools
Each tool has a clearly distinct purpose with no ambiguity. Tools target specific simulation tasks: sequence generation (DNA/protein), evolution (evolve/mutate), phylogeny simulation, and FASTQ file generation. The descriptions clearly differentiate their scopes, preventing misselection.
All tools follow a consistent verb_noun pattern (e.g., evolve_sequence, generate_dna_sequence, simulate_fastq_file). The naming convention is uniform throughout, using snake_case and clear action-object pairs, making the tool set predictable and readable.
With 6 tools, the count is well-scoped for a sequence simulation server. Each tool earns its place by covering key aspects: sequence generation, mutation, evolution, phylogeny, and FASTQ simulation. This provides a focused yet comprehensive surface without being overwhelming.
The tool set covers core sequence simulation workflows effectively, including generation, mutation, evolution, phylogeny, and sequencing data. A minor gap is the lack of tools for analyzing or visualizing simulated data, but agents can work around this as the surface supports essential simulation tasks.