GPU accllerated program for Neighbor-Joining algorithm of Biopython library. The project includes both Serial Vesion and the GPU version of Neighbour Joining Algorithm. I have used PyCUDA API which maps CUDA into Python for the implementation convienience.

Clone or download the .zip file of the project and locate to the root directory.

Inorder to run the program you shold have following hardware and software requirements.

Python 3
Biopython library install
PyCUDA

GPU server

Python 3 - https://www.python.org/downloads/
Biopython - https://biopython.org/wiki/Download
PyCUDA - https://wiki.tiker.net/PyCuda/Installation

After installing above softwares you are good to go.

To run the Serial Version of NJ algorithm run the follwing commands from root directory.

cd Serial-Version
python phylo_treeSerial.py

To run the GPU version of NJ algorithm run the following commands from root directory.

cd GPU-Version
python phylo_treeGPU.py

Test datasets(both Amino Acids and DNA) have been given in Datasets directory. Change the phylo_treeGPU.py file accordingly and test the results for different datasets.