Random local neighbor joining A new method for reconstructing phylogenetic trees》.pdf

Available online at Molecular Phylogenetics and Evolution 47 (2008) 117–128 /locate/ympev Random local neighbor joining: A new method for reconstructing phylogenetic trees Wei Zhang, Zhirong Sun * Institute of Bioinformatics and Systems Biology, MOE Key Laboratory of Bioinformatics, State Key Laboratory of Biomembrane and Membrane Biotechnology, Department of Biological Sciences and Biotechnology, Tsinghua University, Beijing 100084, China Received 5 May 2007; revised 16 December 2007; accepted 22 January 2008 Available online 1 February 2008 Abstract We have developed a new method for reconstructing phylogenetic trees called random local neighbor-joining (RLNJ). Our method is different from the neighbor-joining method (NJ) of Saitou and Nei and affords a more thorough sampling of solution space by randomly searching for local pair of neighbors in each step. Results using the RLNJ method to analyze yeast data show an increasing possibility to get a smaller S value (sum of branch lengths) compared with the NJ method as cases with more taxa are analyzed and many individual runs using the RLNJ method usually generate more than one topology with small S values. Computer simulation shows the fact that the RLNJ method can improve the possibility of recovering correct topology significantly by affording more than one topology. In addition, when using the RLNJ method, computer simulation also shows that the proportion of correct topologies (PC) will increase as the number of different topologies decreases and as the propo