# Phylogenetic Tree Construction AI Agent Connect

> Construct evolutionary trees and calculate genetic distances from sequence alignments.

## Overview
- **Category:** science
- **Price:** Free
- **Endpoint:** https://edge.vinkius.com/vk_preview_y2uJko4bX74PgbLyWmBuwTXBaxZ5sDqUkNmT9IDB/ai-agent-connect
- **Tags:** phylogenetics, evolution, dna, protein, alignment, bioinformatics

## Description

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.

## Tools

### build_distance_tree
Construct a phylogenetic tree using distance-based algorithms

### build_likelihood_tree
Construct a phylogenetic tree using Maximum Likelihood estimation

### calculate_evolutionary_distances
Generate a raw distance matrix from an alignment without building a full tree

### evaluate_tree_reliability
Analyze the statistical confidence and stability of a previously constructed tree

## Prompt Examples

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

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

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

**Response:** 
```
The evolutionary distance matrix has been generated successfully.
```

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

**Response:** 
```
The tree reliability analysis is complete, showing a stability index of 0.85.
```

## Frequently Asked Questions

**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` tool 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.