Phylogenetic tree creation program in Python 3.6.3 using ete3.
This project is a command-line program to visualize phylogenetic trees creation.
For the moment, two building agorithms are available :
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
pypgt <option> <files>
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
- -u : UPGMA method
- -w : WPGMA method
- 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
Example :
pypgt -w examples/simple.phgen # examples folder contains testing files, here I use WPGMA method