Phylogenetic Tree Application

Introduction

This project is a web-based application for visualizing and analyzing phylogenetic trees. It provides an easy-to-use interface for uploading sequences, generating phylogenetic trees, and visualizing evolutionary relationships. The application is particularly useful for researchers and students in the field of evolutionary biology.

Features

• Upload tree files (e.g., Newick or Nexus formats) to generate phylogenetic trees.
• Visual representation of evolutionary relationships.
• User-friendly web interface.

Prerequisites

• Python 3.8 or higher

Installation Instructions

Install pip (if not already installed)

1. Open Command Prompt or Terminal:

   • For Windows, press Win + R, type cmd, and hit Enter.
   • For macOS/Linux, press Cmd + Space, type Terminal, and hit Enter.

2. Install pip:

   • Run the following command to install pip:

     python -m ensurepip --upgrade
     

Windows

1. Open Command Prompt:

   • Press Win + R, type cmd, and hit Enter.

2. Install Python (if not already installed):

   • Download the installer from python.org.
   • Make sure to check "Add Python to PATH" during installation.

3. Clone the repository:

   git clone https://github.com/username/phylogenetic_tree_app.git
   cd phylogenetic_tree_app
   

4. Install virtualenv (if not installed):

   pip install virtualenv
   

5. Create and activate a virtual environment:

   python -m venv venv
   venv\Scripts ctivate
   

6. Install dependencies:

   pip install -r requirements.txt
   

7. Run the application:

   python phylogenetic_tree_app.py
   

macOS/Linux

1. Open Terminal:

   • Press Cmd + Space, type Terminal, and hit Enter.

2. Install Python (if not already installed):

   • Install via Homebrew (recommended):

     /bin/bash -c "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/HEAD/install.sh)"
     brew install python
     

3. Clone the repository:

   git clone https://github.com/username/phylogenetic_tree_app.git
   cd phylogenetic_tree_app
   

4. Install virtualenv (if not installed):

   pip3 install virtualenv
   

5. Create and activate a virtual environment:

   python3 -m venv venv
   source venv/bin/activate
   

6. Install dependencies:

   pip install -r requirements.txt
   

7. Run the application:

   python phylogenetic_tree_app.py
   

Libraries

The project requires the following Python libraries (to be added in requirements.txt):

• Flask: For the web interface.
• Biopython: For biological sequence analysis.
• ete3: For tree visualization and manipulation.
• Werkzeug: For secure file handling.

License

This project is licensed under the MIT License. See the LICENSE file for details.

Contributing

Feel free to submit pull requests or report issues.

Contact

For any questions or suggestions, please contact [[email protected].