EvoTree - Phylogenetic Analysis Tool

A web-based application for phylogenetic analysis using NCBI and UniProt databases. EvoTree allows you to search for proteins and genes, perform sequence alignments, and construct phylogenetic trees through an intuitive web interface.

Features

• Protein Search: Query proteins from UniProt and NCBI databases
• Gene Search: Search for mRNA sequences from NCBI Nucleotide database
• Sequence Selection: Filter sequences by length, database, and other criteria
• Phylogenetic Pipeline: Automated sequence alignment (MAFFT) and tree construction (IQ-TREE)
• Export Options: Download FASTA files and phylogenetic results

Installation

Prerequisites

1. Install Miniconda or Anaconda
   • Download from: https://docs.conda.io/projects/miniconda/en/latest/
   • Follow the installation instructions for your operating system
   • Make sure conda is added to your system PATH
   • Initialize conda: Open a new terminal and run conda init
   • Restart your terminal after initialization

Setup Instructions

1. Download the source code

   • Click on the green "Code" button
   • Select "Download ZIP"
   • Extract the ZIP file

2. Open Anaconda Prompt

   • Navigate to the EvoTree folder you just extracted

   cd C:\EvoTree\

3. Create the conda environment

   conda env create -f environment.yml

   This will create a new conda environment called evotree with all required dependencies.

4. Verify installation

   conda activate evotree
   python --version  # Should show Python 3.11.x

Usage

Starting EvoTree

Option 1: Using the batch file (Windows)

• Simply double-click run_evotree.bat
• The application will start automatically and open in your web browser

Option 2: Manual startup

conda activate evotree
python main.py

Using the Application

1. Search for sequences:

   • Enter a protein or gene name
   • Specify taxonomy (organism name or ID)
   • Choose between protein search (UniProt + NCBI) or gene search (NCBI mRNA)

2. Select and filter sequences:

   • Review results in the interactive table
   • Apply filters by sequence length, database, or mRNA availability
   • Select sequences for phylogenetic analysis

3. Run phylogenetic analysis:

   • Click "Build Phylogenetic Tree" to start the automated pipeline
   • The system will perform sequence alignment and tree construction
   • Download results including FASTA files, alignments, and phylogenetic trees

Stopping EvoTree

• Close the terminal/command prompt window, or
• Press Ctrl+C in the terminal

System Requirements

• Operating System: Windows, macOS, or Linux
• Python: 3.11+ (automatically installed with conda environment)
• Memory: 4GB RAM minimum, 8GB recommended
• Disk Space: 2GB free space for installation
• Internet: Required for database queries (NCBI, UniProt)

Dependencies

Main Dependencies

• NiceGUI: Web-based user interface
• BioPython: Biological sequence analysis
• Requests/HTTPX: HTTP client for API calls
• NumPy/SciPy: Numerical computing
• Matplotlib: Plotting and visualization

External Tools (Server-side)

• MAFFT: Multiple sequence alignment
• IQ-TREE: Maximum-likelihood phylogenetic inference
• BMGE: Block mapping and gathering with entropy (optional)

Troubleshooting

Common Issues

1. Conda environment creation fails

# Initialize conda first if not done
conda init

# Restart terminal, then try with explicit solver
conda env create -f environment.yml --solver=classic

2. Application doesn't start

• Verify conda environment is activated: conda activate evotree
• Check if all dependencies are installed: conda list
• Try running directly: python main.py

3. Browser doesn't open automatically

• Manually navigate to: http://localhost:8080
• Check if port 8080 is available

4. Database connection issues

• Verify internet connection
• Check if NCBI/UniProt services are accessible

5. Server connection issues

• If requests fail, the Flask server might be under maintenance. Please try again later.
• If the issue persists, contact me for further assistance.

Contact

For questions or support, please contact:

• Email: [email protected]
• GitHub: LSMBO/EvoTree