🧬 ClonalTreeClustering

ClonalTreeClustering is a bioinformatics tool designed for clustering B-cell lineage trees. It processes Newick files containing lineage trees, constructs a distance matrix for all node pairs, and builds a map with abundance information for each node. This data is used to perform clustering of B-cell lineage trees using the KMeansSuperTreeClustering program.

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📖 Overview

• Purpose: To construct distance matrices and abundance maps for nodes in lineage trees.
• Input:
  • A Newick file with lineage trees.
  • A FASTA file corresponding to the tree.
  • An integer specifying the number of sequences in the FASTA file.
• Output:
  • Distance matrices between nodes.
  • Abundance maps for nodes in each tree.

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🛠️ Versions

1st Version: V1_ClonalTreeClustering.cpp

• Reads and stores B-cell lineage trees in a C++ data structure.
• Constructs a distance matrix for node pairs.
• Status: Deprecated.

2nd Version: ClonalTreeClustering.cpp

• Reads lineage trees and constructs distance matrices and abundance maps.
• Accepts a single Newick file with one tree, a FASTA file, and the number of sequences as input.
• Future Improvement: The aim is to directly include abundance information in sequence identifiers within the Newick file.

Example Newick Format with Abundance:

(((((([email protected]:1)[email protected]:1)[email protected]:1,...))[email protected]:1);

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✅ Prerequisites

Make sure you have the following tools installed before running ClonalTreeClustering:

• C++ Compiler (e.g., GCC)
• Make Utility

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🚀 How to Compile

1. Navigate to the src directory of the repository:

   cd src

2. Compile the program using the make command:

   make

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🖥️ Usage

Once compiled, run the program with:

./ClonalTreeClustering <newick_file> <fasta_file> <#sequences>

Example:

./ClonalTreeClustering ../data/simulated-data/casX/casX.nk ../data/simulated-data/casX/casX-50.fasta 50

• <newick_file>: Path to the Newick file (e.g., casX.nk).
• <fasta_file>: Path to the FASTA file (e.g., casX-50.fasta).
• <#sequences>: Number of sequences (e.g., 50).

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🧹 Clean-Up

Remove all compiled files and executables with:

make clean

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📄 Notes and Future Plans

• Currently, abundance information is provided separately via a FASTA file and sequence count.
• Future improvements aim to streamline the process by including abundance information directly in sequence identifiers within the Newick file.

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🎯 Example Directory Structure

ClonalTreeClustering/  
│  
├── src/  
│   ├── ClonalTreeClustering.cpp  
│   ├── V1_ClonalTreeClustering.cpp  
│   ├── Makefile  
│  
├── data/  
│   ├── simulated-data/  
│       ├── casX/  
│           ├── casX.nk  
│           ├── casX-50.fasta  
│  
└── README.md  

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🤝 Acknowledgments

This project is developed as part of ongoing research in B-cell lineage tree clustering. Contributions from collaborators in the bioinformatics community are greatly appreciated.