PyPgt

Phylogenetic tree creation program in Python 3.6.3 using ete3.

Description

This project is a command-line program to visualize phylogenetic trees creation.

For the moment, two building agorithms are available :

• UPGMA
• WPGMA

Installation

Place the folder wherever you want in your filesystem, and from the root of the project launch the following commands:

pip3 install -r requirements.txt
echo "alias pypgt='python3 $PWD/src/phylo.py'" >> ~/.bashrc

Using

pypgt <option> <files>

Input format

Input files contain the distance matrix between species that are being analyzed.

These files may be of any extension, content must be formatted this way :

0 1 2
1 0 3
2 3 0

Available options

• -u : UPGMA method
• -w : WPGMA method

Error codes

• 0 : no error
• 1 : input file doesn't contain a square matrix;
• 2 : matrix doesn't contain a diagonal of zeros;
• 3 : matrix isn't a distance matrix (check the ref.)
• 4 : I/O error (input file doesn't exist)
• 5 : matrix is not square
• 6 : values in matrix are not integers

Testing

Example :

pypgt -w examples/simple.phgen # examples folder contains testing files, here I use WPGMA method