MCP For Claude Marketplace
Phylogenetic Tree Construction

Phylogenetic Tree Construction MCP Connector for Claude

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Construct evolutionary trees and calculate genetic distances from sequence alignments.

4 tools Official Updated Oct 1, 2026 Official Vinkius Partner
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This MCP server provides specialized tools for evolutionary biology. It allows AI agents to transform Multiple Sequence Alignments (MSA) into phylogenetic trees using both distance-based methods like build_distance_tree and statistically robust Maximum Likelihood estimation via build_likelihood_tree. Users can also generate raw distance matrices with calculate_evolutionary_distances or validate existing tree structures using evaluate_tree_reliability to ensure statistical confidence in evolutionary relationships.

phylogeneticsevolutiondnaproteinalignmentbioinformatics

4 tools expose this connector's capabilities to your AI agent.

build_distance_tree

Provide a valid alignment and model. Construct a phylogenetic tree using distance-based algorithms

calculate_evolutionary_distances

Provide the alignment and distance model. Generate a raw distance matrix from an alignment without building a full tree

evaluate_tree_reliability

Provide the tree topology, original alignment, and resampling method. Analyze the statistical confidence and stability of a previously constructed tree

build_likelihood_tree

Provide an alignment, substitution model, and bootstrap iterations. Construct a phylogenetic tree using Maximum Likelihood estimation

See how to talk to your AI agent using Phylogenetic Tree Construction.

Build a distance-based phylogenetic tree from this alignment using the Jukes-Cantor model: >seq1 ATGC >seq2 ATGG

The phylogenetic tree has been constructed with the following topology: ((seq1, seq2)).

Calculate the evolutionary distances for this alignment using the Kimura-2-Parameter model: >seq1 ATGC >seq2 ATGG

The evolutionary distance matrix has been generated successfully.

Can you check the reliability of this tree topology: (A:0.1, B:0.2, C:0.3)?

The tree reliability analysis is complete, showing a stability index of 0.85.

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

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