Three-dimensional phylogeny explorer: Distinguishing paralogs, lateral transfer, and violation of "molecular clock" assumption with 3D visualization

BMC Bioinformatics

Volumn 8, Issue , 2007, Pages

  Kim, Namshin ^a   Lee, Christopher ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

EVOLUTIONARY DISTANCE; GENE DUPLICATIONS; LATERAL GENE TRANSFERS; MICROBIAL GENOMES; PHYLOGENETIC TREES; SEQUENCE ALIGNMENTS; TREE VISUALIZATION; WEB-BASED IMPLEMENTATION;

ATOMIC CLOCKS; BIOINFORMATICS; BIOLOGY; DATA VISUALIZATION; GENE TRANSFER; GENES; THREE DIMENSIONAL; THREE DIMENSIONAL COMPUTER GRAPHICS; TOOLS; VISUALIZATION;

TREES (MATHEMATICS);

ARTICLE; GENE CLUSTER; GENE TRANSFER; GENETIC ALGORITHM; GENETIC CONSERVATION; GENETIC DATABASE; GENOME; MOLECULAR CLOCK; PHYLOGENETIC TREE; SEQUENCE ALIGNMENT; THREE DIMENSIONAL IMAGING; WEB BROWSER; BIOLOGICAL MODEL; BIOLOGICAL RHYTHM; CHROMOSOME MAP; COMPUTER GRAPHICS; COMPUTER INTERFACE; COMPUTER PROGRAM; COMPUTER SIMULATION; EVALUATION; GENETICS; METHODOLOGY; MOLECULAR EVOLUTION;

BIOLOGICAL CLOCKS; CHROMOSOME MAPPING; COMPUTER GRAPHICS; COMPUTER SIMULATION; EVOLUTION, MOLECULAR; IMAGING, THREE-DIMENSIONAL; MODELS, GENETIC; SOFTWARE; USER-COMPUTER INTERFACE;

EID: 34447267473     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-8-213     Document Type: Article

References (21)

1. Page RD TreeView: An application to display phylogenetic trees on personal computers Comput Appl Biosci 1996 12 4 357-358 8902363
2. Swofford DL PAUP*: Phylogenetic analysis using parsimony (* and other methods). Sunderland, Mass., Sinauer Associates 2000
3. Zmasek CM Eddy SR ATV: Display and manipulation of annotated phylogenetic trees Bioinformatics 2001 17 4 383-384 10.1093/ bioinformatics/17.4.383 11301314
4. Sanderson MJ Paloverde: An OpenGL 3D phylogeny browser Bioinformatics 2006 22 8 1004-1006 10.1093/bioinformatics/btl044 16500938
5. Lott PL Mundry M Sassenberg C Lorkowski S Fuellen G Simplifying gene trees for easier comprehension BMC Bioinformatics 2006 7 1 231 1473203 16643669 10.1186/1471-2105-7-231
6. Trooskens G De Beule D Decouttere F Van Criekinge W Phylogenetic trees: visualizing, customizing and detecting incongruence Bioinformatics 2005 21 19 3801-3802 10.1093/bioinformatics/bti590 16030069
7. Du Z Lin F Roshan UW Reconstruction of large phylogenetic trees: A parallel approach Comput Biol Chem 2005 29 4 273-280 10.1016/ j.compbiolchem.2005.06.003 16040277
8. Saldanha AJ Java Treeview--extensible visualization of microarray data Bioinformatics 2004 20 17 3246-3248 10.1093/bioinformatics/bth349 15180930
9. Parr CS Lee B Campbell D Bederson BB Visualizations for taxonomic and phylogenetic trees Bioinformatics 2004 20 17 2997-3004 10.1093/ bioinformatics/bth345 15180933
10. Zhai Y Tchieu J Saier MH Jr. A web-based Tree View (TV) program for the visualization of phylogenetic trees J Mol Microbiol Biotechnol 2002 4 1 69-70 11763971
11. Tatusov RL Fedorova ND Jackson JD Jacobs AR Kiryutin B Koonin EV Krylov DM Mazumder R Mekhedov SL Nikolskaya AN Rao BS Smirnov S Sverdlov AV Vasudevan S Wolf YI Yin JJ Natale DA The COG database: An updated version includes eukaryotes BMC Bioinformatics 2003 4 41 222959 12969510 10.1186/1471-2105-4-41
12. Tatusov RL Galperin MY Natale DA Koonin EV The COG database: A tool for genome-scale analysis of protein functions and evolution Nucleic Acids Res 2000 28 1 33-36 102395 10592175 10.1093/nar/28.1.33
13. Tatusov RL Koonin EV Lipman DJ A genomic perspective on protein families Science 1997 278 5338 631-637 10.1126/science.278.5338.631 9381173
14. Tatusov RL Natale DA Garkavtsev IV Tatusova TA Shankavaram UT Rao BS Kiryutin B Galperin MY Fedorova ND Koonin EV The COG database: New developments in phylogenetic classification of proteins from complete genomes Nucleic Acids Res 2001 29 1 22-28 29819 11125040 10.1093/nar/ 29.1.22
15. Koonin EV Orthologs, paralogs, and evolutionary genomics Annu Rev Genet 2005 39 309-338 10.1146/annurev.genet.39.073003.114725 16285863
16. Wheeler DL Barrett T Benson DA Bryant SH Canese K Chetvernin V Church DM DiCuccio M Edgar R Federhen S Geer LY Kapustin Y Khovayko O Landsman D Lipman DJ Madden TL Maglott DR Ostell J Miller V Pruitt KD Schuler GD Sequeira E Sherry ST Sirotkin K Souvorov A Starchenko G Tatusov RL Tatusova TA Wagner L Yaschenko E Database resources of the National Center for Biotechnology Information Nucleic Acids Res 2007 35 Database issue D5-2 1781113 17170002 10.1093/nar/gkl1031
17. Stallmann M Brglez F Ghosh D Heuristics and experimental design for bigraph crossing number minimization Algorithm Engineering and Experimentation Lecture Notes in Computer Science 1999 1619 74-93
18. Chenna R Sugawara H Koike T Lopez R Gibson TJ Higgins DG Thompson JD Multiple sequence alignment with the Clustal series of programs Nucleic Acids Res 2003 31 13 3497-3500 168907 12824352 10.1093/nar/gkg500
19. Retief JD Phylogenetic analysis using PHYLIP Methods Mol Biol 2000 132 243-258 10547839
20. Graham SW Olmstead RG Barrett SC Rooting phylogenetic trees with distant outgroups: A case study from the commelinoid monocots Mol Biol Evol 2002 19 10 1769-1781 12270903
21. Kumar S Molecular clocks: Four decades of evolution Nat Rev Genet 2005 6 8 654-662 10.1038/nrg1659 16136655