What kind of trees can this MCP build?

It can build trees using distance-based algorithms and Maximum Likelihood estimation.

Can I check if my tree is accurate?

Yes, you can use the evaluate_tree_reliability capability to analyze the statistical confidence and stability of a tree.

Do I have to build a tree to get distances?

No, the calculate_evolutionary_distances capability lets you generate a raw distance matrix without building a full tree.

Which AI clients can use this?

You can use this with any MCP-compatible client like Claude, Cursor, or Windsurf.

What data do I need to provide?

You generally need to provide a valid sequence alignment and specify a model for the calculations.

What kind of sequence data can I use?

You can use Multiple Sequence Alignments (MSA) in FASTA format for DNA or protein sequences.

How do I verify if my tree is reliable?

You can use the evaluate_tree_reliability capability to perform statistical validation like bootstrapping on your tree topology.

What is the difference between the tree building methods?

Distance-based methods are faster for large datasets, while Maximum Likelihood methods provide higher statistical accuracy for evolutionary inference.

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Connect Phylogenetic Tree Construction to ChatGPT and Claude

Set it up once and it works in ChatGPT, Claude, Cursor, and any other client you love. It all runs safely in the background, so you can relax and focus on what really matters. Turn sequence alignments into accurate evolutionary trees.

Ask AI about this Connector

Developed, maintained, and hosted by Vinkius.

MCP VERIFIED · PRODUCTION READY · VINKIUS GUARANTEED

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Works with modern AI clients that support MCP, including ChatGPT, Claude, Cursor, and more.

Your AI does the work. We keep it safe and sound.

No other AI tool gives you this. Your workflow runs in the client you already love, your account stays protected, and you decide what the agent can and cannot do. It is the whole reason to make the switch.

Each Connector lives inside our infrastructure, the same place where your workflow runs. The three things below are already part of it, working quietly in the background so you never have to think about them. Nothing to add, nothing to set up, nothing to worry about.

V8 Isolate01

Each Connector runs inside its own sealed environment.

Each Connector runs inside its own sealed V8 runtime — no access to your files, your system, or other servers. A Connector never sees past its own request.

Kill Switch02

One switch stops every agent. Instantly.

One action deactivates every Connector, revokes every token, and ends every session at once. AI Governance keeps the record.

FinOps per User03

Spending limits that pause instead of surprise.

Every user keeps their own connections and credentials, isolated from everyone else. Anything that would cross your spending limit is held for your approval, not billed.

Three controls, built into the layer your AI connects through.

Curated set · 4 capabilities

We ship only the actions that matter.

Capability set01 / 01

01-04

4 capabilities in this set.

Part of 4 available through Phylogenetic Tree Construction.

01
Build distance tree
This capability constructs a phylogenetic tree using distance-based algorithms. You just need to provide a valid alignment and a model.
02
Calculate evolutionary distances
This capability generates a raw distance matrix from an alignment. It's useful when you need the distances without building a full tree.
03
Evaluate tree reliability
This capability analyzes the statistical confidence and stability of a tree you've already built. You'll need to provide the topology, the original alignment, and a resampling method.
04
Build likelihood tree
This capability uses Maximum Likelihood estimation to build trees. It requires an alignment, a substitution model, and bootstrap iterations.

Real work

What teams actually run

Rapid Prototyping

Quickly generate a distance-based tree to get a first look at sequence relationships.

Statistical Validation

Check if a proposed tree topology is stable using reliability analysis.

Distance Matrix Generation

Get raw evolutionary distances for downstream analysis without building a full tree.

High-Confidence Modeling

Use Maximum Likelihood estimation for more robust evolutionary reconstructions.

One connector, every AI

Phylogenetic Tree Construction works with the most popular AI clients.

These are the most popular clients, each with a step-by-step guide: one link, set up once, with governance and visibility built in. And because everything runs on the MCP standard, the same connection also works in any other compatible client — nothing to rebuild.

Building your own app? The connector is yours to use.

You don't need a client to put Phylogenetic Tree Construction to work: the same hosted connection plugs into your own applications and agent code, with the same governance on every request. Build with it, chat with it — one connection for both.

Observed, not estimated

906ms average. Fast in production.

Phylogenetic Tree Construction is checked daily against the live service.

Daily averagePeak 1208ms

Oct 3Today

Fastest day: 665ms
Slowest day: 1208ms
14-day trend: Slowing+31%

Connect your client

One URL. Every client.

Activate the Connector, copy your link, and paste it into the client you already use. 4 capabilities arrive ready to run.

Preview access · not provider authentication

The vk_preview_* token belongs to Vinkius preview infrastructure. It lets Claude discover and display the capabilities of Phylogenetic Tree Construction, so you can see the experience inside your AI.

It does not authenticate your account with Phylogenetic Tree Construction. Actions requiring credentials or live account data may not run until you activate the Connector and authorize the service.

Phylogenetic Tree Construction Connector

You're all set. Choose your MCP client and follow the setup instructions.

Connector linkhttps://edge.vinkius.com/vk_preview_y2uJko4bX74PgbLyWmBuwTXBaxZ5sDqUkNmT9IDB/mcp

Claude Desktop

Follow the steps below to connect in seconds.

1In Claude Desktop, open Settings → Connectors.
2Click “Add custom connector” and paste the connector link above as the remote MCP server URL.
3Click Add and start a new chat — Phylogenetic Tree Construction capabilities are ready to use.

Configuration · claude_desktop_config.jsonCopy

{
  "mcpServers": {
    "phylogenetic-tree-construction-mcp": {
      "url": "https://edge.vinkius.com/vk_preview_y2uJko4bX74PgbLyWmBuwTXBaxZ5sDqUkNmT9IDB/mcp"
    }
  }
}

Claude
ChatGPT
Cursor
VS Code
Windsurf
Claude Code
JetBrains
Cline

Step-by-step instructions for each client are in the guide. How to connect

Guided setup for Claude? Set up Phylogenetic Tree Construction in Claude and other AIs

See all the AI clients this connector works with ↑

Who it's for

Built for the work Phylogenetic Tree Construction owners hand off.

This MCP is built for researchers and developers working in bioinformatics and evolutionary biology.

01
Bioinformaticians
They hand off sequence alignments to the AI to automate tree building and distance calculations.
02
Evolutionary Biologists
They use the capability to validate the statistical confidence of their evolutionary models.
03
Computational Biologists
They integrate these capabilities into larger automated pipelines via their AI agents.

FAQ

Questions Phylogenetic Tree Construction owners ask.

01
What kind of trees can this MCP build?
It can build trees using distance-based algorithms and Maximum Likelihood estimation.
02
Can I check if my tree is accurate?
Yes, you can use the evaluate_tree_reliability capability to analyze the statistical confidence and stability of a tree.
03
Do I have to build a tree to get distances?
No, the calculate_evolutionary_distances capability lets you generate a raw distance matrix without building a full tree.
04
Which AI clients can use this?
You can use this with any MCP-compatible client like Claude, Cursor, or Windsurf.
05
What data do I need to provide?
You generally need to provide a valid sequence alignment and specify a model for the calculations.
06
What kind of sequence data can I use?
You can use Multiple Sequence Alignments (MSA) in FASTA format for DNA or protein sequences.
07
How do I verify if my tree is reliable?
You can use the evaluate_tree_reliability capability to perform statistical validation like bootstrapping on your tree topology.
08
What is the difference between the tree building methods?
Distance-based methods are faster for large datasets, while Maximum Likelihood methods provide higher statistical accuracy for evolutionary inference.

Explore

More in Science

Connect Phylogenetic Tree Construction to Claude, Cursor, ChatGPT & more

Your AI does the work. We keep it safe and sound.

Each Connector runs inside its own sealed environment.

One switch stops every agent. Instantly.

Spending limits that pause instead of surprise.

We ship only the actions that matter.

01-04

Build distance tree

Calculate evolutionary distances

Evaluate tree reliability

Build likelihood tree

What teams actually run

Rapid Prototyping

Statistical Validation

Distance Matrix Generation

High-Confidence Modeling

Building your own app? The connector is yours to use.

Phylogenetic Tree Construction Connector

Claude Desktop

Bioinformaticians

Evolutionary Biologists

Computational Biologists

What kind of trees can this MCP build?

Can I check if my tree is accurate?

Do I have to build a tree to get distances?

Which AI clients can use this?

What data do I need to provide?

What kind of sequence data can I use?

How do I verify if my tree is reliable?

What is the difference between the tree building methods?

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