Date: 19 May 2008 (Monday)
Time: 2:30am - 5:30pm
Venue: Room 232, Lady Shaw Building, CUHK
Abstract: The complete genomes of living organisms have provided much information on their phylogenetic relationships. Similarly, the complete genomes of the chloroplast and mitochondria have helped to resolve the evolution of these organelles in photosynthetic eukaryotes and vertebrates respectively. Existing tools and traditional sequence distance methods for phylogenetic analysis, e.g., multiple alignment and various sequence evolutionary models, do not directly apply to complete genomes. Some distance methods without alignment have been developed for phylogenetic analysis using complete genomes. In this talk we will show some distance methods without sequence alignment based on SVD method, Markov model, dynamical language model, Fourier method and log-correlation distance, Entropy density profile with log-correlation distance, mutual information distance. The above distance methods have been used to analyse the phylogenetic relationship of bacteria, viruses and vertebrates based on the genomes. The results are largely in agreement with the current understanding on these organisms.
