# NewickToMatrix Conversion v0.1

**Authors**: UQAM Lab  
**Date**: June 2009

### 📜 Description:
The `NewickToMatrix` program converts lineage trees represented in Newick format into distance matrices. The program computes tree distances based on the **GLBD metric**. This utility is ideal for comparing lineage trees and analyzing the relationships between them in a structured manner.

### 🧰 Requirements:
- 🐧**Linux** or UNIX-based system
- 🖥️**C++ Compiler** (any standard C++ compiler)

### 🔨 How to Compile the Program:

To compile the `NewickToMatrix` program, use the following command on a Linux/UNIX system:

```bash
c++ NewickToMatrix.cpp -o n2m

This will create the executable n2m to run the program.

🏃‍♂️ How to Run the Program:

The program can process multiple input files containing Newick sequences or a single file with multiple sequences. The format of the input is determined by the command-line argument passed.

Command Syntax:

1. Single File with Multiple Newick Sequences:

./n2m -s X input_file output_file.txt

Where X is the number of sequences in input_file, and output_file.txt is the destination for the resulting distance matrix.

2. Multiple Files with One Newick Sequence Each:

./n2m -m file1 file2 output_file.txt

This command allows you to provide multiple files, each containing one Newick sequence.

⚠️ Important Notes:

• Node names cannot contain the word "node" as this will prevent comparisons between trees.
• Ensure that your Newick sequences are correctly formatted before running the program.

📝 Output File:

The output_file.txt will contain:

1. The distance matrix for each lineage tree.
2. A comparison matrix between all trees.

The format of the output will be as follows:

Example Output for Individual Distance Matrices:

tree_1    number of nodes: 12

Comparison Matrix:

The comparison matrix lists the distance between each tree. A value of -1.0 indicates that the trees have fewer than 3 nodes in common and were not compared.

Example:

Comparison Matrix
tree_1    0.000000    13.228757    7.681146    -1.0
tree_2    13.228757   0.000000     14.966630   -1.0
tree_3    7.681146    14.966630    0.000000    -1.0
tree_4    -1.0        -1.0         -1.0         0.000000

🛠️ How it Works:

The program first reads Newick sequences, processes the lineage trees, and then computes the pairwise distances between them using the GLBD metric. It stores the resulting distances in a matrix and outputs this information into the specified output file.

1. Input Handling: The program can handle both single and multiple files containing Newick sequences.
2. Distance Calculation: For each pair of trees, the distance is computed and stored.
3. Output: The results are saved in a matrix format, making it easy to analyze the distances and relationships between the trees.

🔄 Future Improvements:

• Add more distance metrics for comparison.
• Improve error handling for malformed Newick sequences.

👨‍💻 Contributors:

• UQAM Lab for developing and maintaining the code.