Tuyển tập các báo cáo nghiên cứu về sinh học được đăng trên tạp chí y học Molecular Biology cung cấp cho các bạn kiến thức về ngành sinh học đề tài: On the use of cartographic projections in visualizing phylo-genetic tree space. | Sundberg et al. Algorithms for Molecular Biology 2010 5 26 http content 5 1 26 AMR ALGORITHMS FOR MOLECULAR BIOLOGY RESEARCH Open Access On the use of cartographic projections in visualizing phylo-genetic tree space Kenneth Sundberg Mark Clement Quinn Snell Abstract Phylogenetic analysis is becoming an increasingly important tool for biological research. Applications include epidemiological studies drug development and evolutionary analysis. Phylogenetic search is a known NP-Hard problem. The size of the data sets which can be analyzed is limited by the exponential growth in the number of trees that must be considered as the problem size increases. A better understanding of the problem space could lead to better methods which in turn could lead to the feasible analysis of more data sets. We present a definition of phylogenetic tree space and a visualization of this space that shows significant exploitable structure. This structure can be used to develop search methods capable of handling much larger data sets. Background Phylogenetic analysis has become an integral part of many biological research programmes. These include such diverse areas as human epidemiology 1 2 viral transmission 3 4 and biogeography 5 . With the advent of new automated sequencing techniques the ability to generate data for inferring evolutionary histories phylogenies for a great diversity of organisms has increased dramatically. Researchers are now commonly generating many sequences from many individuals. However our ability to analyze the data has not kept pace with data generation. Phylogenetic search is a difficult problem. When parsimony is used as the optimality criterion the problem is known to be NP-complete 6 . The search problem itself independent of scoring is known to be NP-Hard 7 . This means that optimal phylogenetic searches on even hundreds of taxa will take years to complete and heuristic searches for near optimal trees must be used. A variety of heuristic .
