https://github.com/kris96tian/phylogenetic_tree_generator

Web App for constructing phylogenetic trees using various clustering methods and algorithms.
https://github.com/kris96tian/phylogenetic_tree_generator

clustering-trees distance-matrix evolutionary-algorithms maximum-parsimony neighbor-joining phylogenetic-trees phylogenetics upgma-clustering

Last synced: 24 days ago
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Web App for constructing phylogenetic trees using various clustering methods and algorithms.

• Host: GitHub
• URL: https://github.com/kris96tian/phylogenetic_tree_generator
• Owner: kris96tian
• Created: 2024-04-09T17:37:51.000Z (about 1 year ago)
• Default Branch: main
• Last Pushed: 2024-12-05T00:52:19.000Z (6 months ago)
• Last Synced: 2024-12-05T01:27:48.670Z (6 months ago)
• Topics: clustering-trees, distance-matrix, evolutionary-algorithms, maximum-parsimony, neighbor-joining, phylogenetic-trees, phylogenetics, upgma-clustering
• Language: HTML
• Homepage: https://clustering.pythonanywhere.com/
• Size: 139 KB
• Stars: 0
• Watchers: 1
• Forks: 0
• Open Issues: 0
• Metadata Files:
  • Readme: README.md

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README

        
# Phylogenetic Tree Builder

![image](https://github.com/user-attachments/assets/0d78be74-31cb-46ab-addc-22efb427a027)

Phylogenetic Tree Builder is a Python application built using the Flask-Framework. It provides functionalities for constructing phylogenetic trees using various clustering methods and algorithms.

## Features

- **Hierarchical Clustering**: Perform hierarchical clustering analysis with different methods such as single, complete, average (UPGMA), weighted, centroid, median, and ward.

- **Neighbor-Joining**: Generate Neighbor-Joining trees, a bottom-up clustering method for creating phylogenetic trees.

- **Maximum Parsimony**: Infer phylogenetic trees by minimizing the total number of evolutionary changes required to explain observed sequence data.

## Usage

1. **Select Method/Algorithm**: Choose the desired clustering method or algorithm from the sidebar menu.

2. **Input Data**: Provide the required data based on the selected method:

   - For Hierarchical Clustering: Enter the number of taxa, taxa names, distances, and select a clustering method.

   - For Neighbor-Joining: Enter the number of taxa, taxa names, and distances.

   - For Maximum Parsimony: Enter the number of DNA sequences and input the sequences.

3. **Perform Analysis**: Click on the corresponding button to perform the analysis.

4. **Explore Results**: Explore the generated dendrogram plots, Neighbor-Joining trees, or Maximum Parsimony trees.

## Clustering Methods

- **Hierarchical Clustering**: Hierarchical clustering is a method of cluster analysis that builds a hierarchy of clusters by merging the closest pairs of clusters.

- **Neighbor-Joining**: The Neighbor-Joining algorithm is a bottom-up (agglomerative) clustering method for creating phylogenetic trees.

- **Maximum Parsimony**: Maximum Parsimony minimizes the total number of evolutionary changes required to explain observed sequence data.