A collection of programs that perform useful tasks and exercises in bioinformatics, many of which have been relevant to my graduate research work. Topics covered include:
- Information theory fundamentals: Shannon entropy, KL-divergence, mutual information, etc.
- Binary searches for nucleic acid polymers
- De bruijn graphs for analyzing nucleic acid k-mers
- Prefix trees / Tries for analyzing nucleic acid k-mers
- Cellular automata
- Longest substring algorithms
- Markov chains
- Hidden markov models (HMMs)
- Fasta & csv file processing