kris96tian/phylogenetic_tree_generator

Web App for constructing phylogenetic trees using various clustering methods and algorithms.

Phylogenetic Tree Builder

Phylogenetic Tree Builder is a Python application built using Streamlit. 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.

Technologies Used

• Streamlit: Used for building the user interface and hosting the application.
• Python Libraries: Including NumPy, Matplotlib, SciPy, Biotite, and BioPython for performing phylogenetic analysis and visualization.

Contributing

Contributions are welcome! If you'd like to contribute to the Phylogenetic Tree Builder by adding new features, fixing bugs, or improving documentation, please open an issue or submit a pull request.