High performance computing for computational biology

Abstract

Both sequence comparison and phylogenetic inference are of great importance to biologists; and these problems are fundamentally interdependent. Most methods for phylogenetic inference use a given sequence alignment as an input, and efficient multiple alignment procedures often take advantage of a phylogenetic relationship of the sequences. However, the algorithms used in these problems are very computationally demanding. Also, the huge increase in size of publicly available genomic data has meant that many common tasks in bioinformatics are not possible to complete in a reasonable amount of time on a single processor. For example, inferring phylogenetic trees is an enormously difficult problem because of the huge number of potential alternative tree topologies, for that number grows exponentially.