This is the repository for my solutions for the 2024-2025 Computational Biology course at ETH Zürich. The course was held by Dr. Timothy Vaughan, Dr. Carsten Magnus, and Prof. Dr. Tanja Stadler. The solutions contain my own implementations on top of the prewritten part that I received from the lecturers.
- Project 1: Implementation of Smith-Waterman and Needleman-Wunsch algorithms for local and global sequence alignments.
- Project 2: Simulation of an alignment of arbitrary length under the TN93 substitution rate with an arbitrary mean substitution rate on a given tree.
- Project 3: Implementation of the UPGMA algorithm to reconstruct an ultrametric tree given the alignment of the sequences. Works both with Humming distance, distance under JC69 model, and distance under K80 model.
- Project 4: Implementation of Felsenstein's tree pruning algorithm to compute the likelihood of an arbitrary alignment on a given tree under the TN93 model.
- Project 5: Implementation of the independent contrast method to determine correlations between continuous traits such as height and weight between individuals/species that have shared evolutionary history.