BranchClust: A phylogenetic algorithm for selecting gene families

BMC Bioinformatics

Volumn 8, Issue , 2007, Pages

  Poptsova, Maria S ^a   Gogarten, J Peter ^a  

^a UNIVERSITY OF CONNECTICUT   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

AUTOMATED METHODS; AUTOMATED SELECTION; BRANCHING ORDER; GENE FAMILIES; ORTHOLOGOUS GENES; PHYLOGENETIC APPROACH; PHYLOGENETIC TREES; SEQUENCE SIMILARITY;

ALGORITHMS; BIOINFORMATICS; GENES;

TREES (MATHEMATICS);

ALGORITHM; ARTICLE; CONTROLLED STUDY; MULTIGENE FAMILY; NONHUMAN; ORTHOLOGY; PARALOGY; PHYLOGENETIC TREE; PHYLOGENY; PROKARYOTE; TAXON; CLUSTER ANALYSIS; COMPUTER PROGRAM; DNA SEQUENCE; GENETICS; METHODOLOGY; MOLECULAR EVOLUTION; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; SEQUENCE ALIGNMENT; SEQUENCE HOMOLOGY;

PROKARYOTA;

PROTEOME;

ALGORITHMS; BASE SEQUENCE; CLUSTER ANALYSIS; CONSERVED SEQUENCE; EVOLUTION, MOLECULAR; MOLECULAR SEQUENCE DATA; MULTIGENE FAMILY; PHYLOGENY; PROTEOME; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS, DNA; SEQUENCE HOMOLOGY, AMINO ACID; SOFTWARE;

EID: 34247324752     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-8-120     Document Type: Article

References (46)

1. Fitch WM Homology a personal view on some of the problems Trends Genet 2000 16 5 227-231 10.1016/S0168-9525(00)02005-9 10782117
2. Koonin EV Orthologs, paralogs, and evolutionary genomics Annu Rev Genet 2005 39 309-338 10.1146/annurev.genet.39.073003.114725 16285863
3. Altschul SF Gish W Miller W Myers EW Lipman DJ Basic local alignment search tool J Mol Biol 1990 215 3 403-410 2231712
4. Altschul SF Koonin EV Iterated profile searches with PSI-BLAST--a tool for discovery in protein databases Trends Biochem Sci 1998 23 11 444-447 10.1016/S0968-0004(98)01298-5 9852764
5. Eddy SR Profile hidden Markov models Bioinformatics 1998 14 9 755-763 10.1093/bioinformatics/14.9.755 9918945
6. Koski LB Golding GB The closest BLAST hit is often not the nearest neighbor J Mol Evol 2001 52 6 540-542 11443357
7. Zhaxybayeva O Gogarten JP Bootstrap, Bayesian probability and maximum likelihood mapping: Exploring new tools for comparative genome analyses BMC Genomics 2002 3 1 4 100357 11918828 10.1186/1471-2164-3-4
8. Montague MG Hutchison CA 3rd Gene content phylogeny of herpesviruses Proc Natl Acad Sci U S A 2000 97 10 5334-5339 25829 10805793 10.1073/ pnas.97.10.5334
9. Zhaxybayeva O Gogarten JP An improved probability mapping approach to assess genome mosaicism BMC Genomics 2003 4 1 37 222983 12974984 10.1186/ 1471-2164-4-37
10. Sonnhammer EL Koonin EV Orthology, paralogy and proposed classification for paralog subtypes Trends Genet 2002 18 12 619-620 10.1016/ S0168-9525(02)02793-2 12446146
11. Vogler AP Homma M Irikura VM Macnab RM Salmonella typhimurium mutants defective in flagellar filament regrowth and sequence similarity of FliI to F0F1, vacuolar, and archaebacterial ATPase subunits J Bacteriol 1991 173 11 3564-3572 207973 1646201
12. Charlebois RL Doolittle WF Computing prokaryotic gene ubiquity: Rescuing the core from extinction Genome Res 2004 14 12 2469-2477 534671 15574825 10.1101/gr.3024704
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. Perriere G Duret L Gouy M HOBACGEN: Database system for comparative genomics in bacteria Genome Res 2000 10 3 379-385 311423 10720578 10.1101/gr.10.3.379
15. Zmasek CM Eddy SR A simple algorithm to infer gene duplication and speciation events on a gene tree Bioinformatics 2001 17 9 821-828 10.1093/bioinformatics/17.9.821 11590098
16. O'Brien KP Remm M Sonnhammer EL Inparanoid: A comprehensive database of eukaryotic orthologs Nucleic Acids Res 2005 33 Database issue D476-80 540061 15608241 10.1093/nar/gki107
17. Remm M Storm CE Sonnhammer EL Automatic clustering of orthologs and in-paralogs from pairwise species comparisons J Mol Biol 2001 314 5 1041-1052 10.1006/jmbi.2000.5197 11743721
18. Chevenet F Brun C Banuls AL Jacq B Christen R TreeDyn: Towards dynamic graphics and annotations for analyses of trees BMC Bioinformatics 2006 7 439 1615880 17032440 10.1186/1471-2105-7-439
19. BranchClust: A phylogenetic algorithm for selecting gene families http://www.bioinformatics.org/branchclust
20. Winstanley C Hart CA Type III secretion systems and pathogenicity islands J Med Microbiol 2001 50 2 116-126 11211218
21. Dobrindt U Hochhut B Hentschel U Hacker J Genomic islands in pathogenic and environmental microorganisms Nat Rev Microbiol 2004 2 5 414-424 10.1038/nrmicro884 15100694
22. Murzin AG Brenner SE Hubbard T Chothia C SCOP: A structural classification of proteins database for the investigation of sequences and structures J Mol Biol 1995 247 4 536-540 10.1006/jmbi.1995.0159 7723011
23. Feng DF Doolittle RF Progressive sequence alignment as a prerequisite to correct phylogenetic trees J Mol Evol 1987 25 4 351-360 10.1007/ BF02603120 3118049
24. Enright AJ Van Dongen S Ouzounis CA An efficient algorithm for large-scale detection of protein families Nucleic Acids Res 2002 30 7 1575-1584 101833 11917018 10.1093/nar/30.7.1575
25. van Dongen S Graph clustering by flow simulation PhD thesis University of Utrecht 2000
26. Harlow TJ Gogarten JP Ragan MA A hybrid clustering approach to recognition of protein families in 114 microbial genomes BMC Bioinformatics 2004 5 45 420232 15115543 10.1186/1471-2105-5-45
27. Gogarten JP Doolittle WF Lawrence JG Prokaryotic evolution in light of gene transfer Mol Biol Evol 2002 19 12 2226-2238 12446813
28. Ochman H Lawrence JG Groisman EA Lateral gene transfer and the nature of bacterial innovation Nature 2000 405 6784 299-304 10.1038/35012500 10830951
29. Felsenstein J Cases in which parsimony and compatibility methods will be positively misleading Syst Zool 1978 27 401-410 10.2307/2412923
30. Gogarten JP Taiz L Evolution of proton pumping ATPases: Rooting the tree of life Photosynthesis Research 1992 33 137-146 10.1007/BF00039176
31. Raymond J Zhaxybayeva O Gogarten JP Gerdes SY Blankenship RE Whole-genome analysis of photosynthetic prokaryotes Science 2002 298 5598 1616-1620 10.1126/science.1075558 12446909
32. Lake JA Herbold CW Rivera MC Servin JA Skophammer RG Rooting the tree of life using nonubiquitous genes Mol Biol Evol 2007 24 1 130-6 10.1093/ molbev/msl140 17023560
33. Zhaxybayeva O Lapierre P Gogarten JP Ancient gene duplications and the root(s) of the tree of life Protoplasma 2005 227 1 53-64 10.1007/ s00709-005-0135-1 16389494
34. Tsutsumi S Denda K Yokoyama K Oshima T Date T Yoshida M Molecular cloning of genes encoding major two Subunits of a eubacterial V-Type ATPase from Thermus thermophilus Biochimica et Biophysica Acta 1991 1098 1 13-20 10.1016/0005-2728(91)90003-7 1836357
35. Hilario E Gogarten JP Horizontal transfer of ATPase genes--the tree of life becomes a net of life Biosystems 1993 31 2-3 111-119 10.1016/ 0303-2647(93)90038-E 8155843
36. Olendzenski L Liu L Zhaxybayeva O Murphey R Shin DG Gogarten JP Horizontal transfer of archaeal genes into the Deinococcaceae: Detection by molecular and computer-based approaches J Mol Evol 2000 51 6 587-599 11116332
37. Lapierre P Shial R Gogarten JP Distribution of F- and A/V-type ATPases in Thermus scotoductus and other closely related species Syst Appl Microbiol 2006 29 1 15-23 10.1016/j.syapm.2005.06.004 16423651
38. Oshima K Kakizawa S Nishigawa H Jung HY Wei W Suzuki S Arashida R Nakata D Miyata S Ugaki M Namba S Reductive evolution suggested from the complete genome sequence of a plant-pathogenic phytoplasma Nat Genet 2004 36 1 27-29 10.1038/ng1277 14661021
39. Fulton DL Li YY Laird MR Horsman BG Roche FM Brinkman FS Improving the specificity of high-throughput ortholog prediction BMC Bioinformatics 2006 7 270 1524997 16729895 10.1186/1471-2105-7-270
40. Dagan T Martin W The tree of one percent Genome Biol 2006 7 10 118 1794558 17081279 10.1186/gb-2006-7-10-118
41. Thompson JD Higgins DG Gibson TJ CLUSTAL W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 1994 22 4673-44680 308517 7984417 10.1093/nar/22.22.4673
42. Edgar RC MUSCLE: A multiple sequence alignment method with reduced time and space complexity BMC Bioinformatics 2004 5 113 517706 15318951 10.1186/1471-2105-5-113
43. Guindon S Gascuel O A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood Syst Biol 2003 52 5 696-704 10.1080/10635150390235520 14530136
44. Schmidt HA Strimmer K Vingron M von Haeseler A TREE-PUZZLE: Maximum likelihood phylogenetic analysis using quartets and parallel computing Bioinformatics 2002 18 3 502-504 10.1093/bioinformatics/18.3.502 11934758
45. Saitou N Nei M The neighbor-joining method: A new method for reconstructing phylogenetic trees Mol Biol Evol 1987 4 4 406-425 3447015
46. Gogarten JP Kibak H Dittrich P Taiz L Bowman EJ Bowman BJ Manolson MF Poole RJ Date T Oshima T Evolution of the vacuolar H+-ATPase: implications for the origin of eukaryotes Proc Natl Acad Sci U S A 1989 86 17 6661-6665 297905 2528146 10.1073/pnas.86.17.6661