Development of computer software for molecular evolutionary analysis

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In this research project, we have aimed at development and unification of computer programs for molecular evolutionary analysis of genetic information. We have also applied the unified programs to nucleotide sequence data to elucidate molecular evolutionary aspects of some viruses. The outcomes from the three year endeavor are four folds.(1) We have developed an integrated computer software system for molecular evolutionary analysis of genetic information which works on a work-station. This system considerably enables us to individually retrieve and analyze on large amounts of DNA data at a high speed. It also operates in a network computer system. (2) A molecular phylogeny estimation method has been devised. This method feeds on nucleotide sequence data from species, and produces plural estimates of the molecular tree for the species. The method was proved, by computer simulation, to work well under certain conditions. (3) We have determined the genome structure of Japanese encephalitis virus. The genome has been revealed to be made up of three structural genes and several non-structural genes. (4) A method for multiple alignment of nucleotide sequences has been developed by use of the dynamic programming. This method makes it possible to simultaneously align 50 sequences at most which may consist of 4,000 nucleotides each.