To understand the patterns and processes underlying the evolutionary dynamics of multigene families, genomes, and model organisms and their close relatives, it is crucial to to develop easy-to-use computer tools for comparative sequence analysis. The investigator proposes to develop Molecular Evolutionary Genetic Analysis 2 (MEGA2) for examining sequences from different perspectives. MEGA2 will support analysis of (1) sequence and polymorphism data, as well as restriction site, allele frequency, and microsatellite data; (2) allow specifications of domains and genes (collections of domains) for comparative analysis; (3) allow for creation of groups of sequences for multigene family and higher level phylogenetic analysis; (4) establish new graphics standards for data representation; (5) provide intuitive sequence alignment construction with emphasis on alignment to genomic sequences; (6) implement existing and develop new computational and statistical methods for sequence data in an easy-to-use, consistent framework. MEGA2 will include programs for estimating evolutionary distances, computing genetic diversity within and among groups of sequences, inferring and testing evolutionary trees, conducting molecular clock tests, inferring ancestral molecular sequences, and testing a variety of evolutionary hypotheses by the bootstrap technique, among other statistical methods.
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