Bioinformatics Coursework (Baum-Welch and Amalgamating Rooted Phylogenetic Trees)

Submitted as part of the degree of Bsc Natural Sciences (3rd year) to the Board of Examiners in the Department of Computer Sciences, Durham University. This summative assignment was assessed and marked by the professor of the module in question:

Grade: 1st - 100/100, 1rd in year (of 116 students).

Paper Introduction:

Coursework implementing the Baum-Welch algorithm, discussion of implementation choices (normalising alpha and beta values, working in log space, parallelization etc.), verification of correctness, in addition to answers to problem sheets on different techniques for amalgamating rooted phylogenetic trees.

Contents of repo:

• report.pdf - Report outlining project.
• Baum-Welch.py - Baum-Welch implementation, Baum-Welch implementation in log space and verification code.

Demo video

Plot demonstrating convergence of log-likelihodd