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1、 36 生 物 信 息 學 第 10 卷 14 House,Christopher H and Sorel T Fitz Gibbon Using Homolog Groups to Create a Whole Genomic Tree of Free Living Organisms: An Update J Journal of Molecular Evolution, 2002 , 54 : 539 547 15 Dandekar,Thomas,Berend Snel,Martijn Huynen,and Peer Bork Conservation of gene order: a

2、fingerprint of proteins that physically interactJ Trends in Biochemical Sciences,1998 , 23 : 324 328 16 Korbel,Jan O ,Berend Snel,Martijn A Huynen,and Peer Bork SHOT: a web server for the construction of genome phylogenies J Trends in Genetics, 2002 , 18 : 158 162 17 Tekaia,F(xiàn)redj,Antonio Lazcano,and

3、 Bernard Dujon The Genomic Tree as Revealed from Whole Proteome ComparisonsJ 1999 , 9 : 550 557 Genome Research, 18 Caetano Anollés,Gustavo and Derek Caetano Anollés An Evolutionarily Structured Universe of Protein ArchitectureJ Genome Research, 2003 , 13 : 1563 1571 19 Yang,S ,R F Doolitt

4、le,and P E Bourne Phylogeny determined by protein domain contentJ Proceedings of the National Academy of Sciences of the United States of America, 2005 , 102 : 373 378 20 Deeds, E J , H Hennessey, and E I Shakhnovich Prokaryotic phylogenies inferred from protein structural domains J Ge2005 , 15 : 39

5、3 402 nome Research, 21 Fukami Kobayashi Kaoru,Yoshiaki Minezaki,Yoshio Tateno, 23 Ken Nishikawa A tree of life based on protein domain organizationsJ Molecular Biology and Evolution,2007 , 24 : 1181 1189 22 Lin, J and M Gerstein Whole genome trees based on the occurrence of folds and orthologs: Imp

6、lications for comparing genomes on different levelsJ Genome Research,2000 , 10 : 808 818 Gough,Julian,Kevin Karplus,Richard Hughey, and Cyrus Chothia Assignment of homology to genome sequences using a library of hidden Markov models that represent all proteins of Journal of Molecular Biology,2001 ,

7、313 : known structureJ 903 919 24 Saitou,N and M Nei The neighbor joining method: a new Molecular Biolmethod for reconstructing phylogenetic treesJ 1987 , 4 : 406 425 ogy and Evolution, 25 Felsenstein,J PHYLIP ( Phylogeny Inference Package ) version 3 6 Distributed by the author Department of Genome Sciences J University of Washington,Seattle, 2004 , 26 Robinson,D F and L R Foulds Comparison of phylogenetic Mathematical Biosciences, 1981 , 53 : 131 147 treesJ 27 Tamura,Koichiro,Joel Dudley,Masatoshi Nei,Sudhir Kumar MEGA4 : Molec

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