Predicting taxonomic identities with codon usage at phylum level with machine learning methods

---

Project for CE9010 at School of Computer Science and Engineering, Nanyang Technological University

Obtained A+ grade overall for the module.

Data obtained from: Using codon usage to predict taxonomic identities of organisms using data from Codon and Codon-Pair Usage Tables (CoCoPUTs) (doi: 10.1016/j.jmb.2019.04.021).

Group Member:

Ng Yong Zhi

Packages used:

• Python=3.9
• wget
• requests
• selenium
• biopython
• pandas
• scikit-learn
• matplotlib
• xgboost

Conda environment

If you have conda installed, you can install the environment used in this analysis by cloning the repository and running conda env create -f environment.yml. Else, ensure your python version is 3.9 and run the first line in the project notebook to install the required packages.