Improvements to BioJava including Implementation of Multiple Sequence Alignment Algorithms

by Mark Chapman for Open Bioinformatics Foundation

Biologists infer evolutionary, structural, and functional relationships between biopolymers from similarities and divergences of primary structure in multiple sequence alignments. I plan to code a module for BioJava which manages an alignment and offers several implementation options. Addition of this framework to BioJava would assist Java-based bioinformatics tools as a reference version of current techniques and as a foundation on which to research variations of multiple sequence alignment.