Molecular Phylogenetic Analysis using both DNA and Amino Acid Sequence Data and Its Parallelization

Hideo Matsuda (
Hiroshi Yamashita (
Yukio Kaneda (

Department of Computer and Systems Engineering,
Faculty of Engineering, Kobe University
1-1 Rokkodai, Nada, Kobe 657 Japan


Phylogenetc analysis of DNA sequences has played an important role in the study on evolution of life. However recent researches suggest that in some cases phylogenetic analysis of protein sequences is more important than that of DNA sequences. Thus we developed a system for phylogenetic analysis of protein sequence data. Since this system is based on our previously developed system for the analysis of DNA sequence data, one can obtain both protein-based and DNA-based trees and compare them. In the two systems, we took the same tree-construction algorithm (so called, a maximum likelihood method). Although this method has concrete models of the evolutionary process, it requires a huge amount of computational costs especially in the analysis of protein sequence data. Therefore we parallelized tree-construction steps in our method on a massively parallel machine.