Inferring genome trees by using a filter to eliminate phylogenetically discordant sequences and a distance matrix based on mean normalized BLASTP scores

Journal of Bacteriology

Volumn 184, Issue 8, 2002, Pages 2072-2080

  Clarke, G D Paul ^a   Beiko, Robert G ^a   Ragan, Mark A ^a   Charlebois, Robert L ^a  

^a UNIVERSITY OF QUEENSLAND   (Australia)

Author keywords

[No Author keywords available]

Indexed keywords

RNA 16S;

ARCHAEBACTERIUM; ARTICLE; BACTERIUM; EUKARYOTE; GENE SEQUENCE; GENETIC DISTANCE; GENOME; NONHUMAN; OPEN READING FRAME; PHYLOGENY; PRIORITY JOURNAL;

DATABASES, PROTEIN; GENOME, BACTERIAL; OPEN READING FRAMES; PHYLOGENY; RNA, RIBOSOMAL, 16S;

ARCHAEA; BACTERIA (MICROORGANISMS); EUKARYOTA; SACCHAROMYCES; SACCHAROMYCES CEREVISIAE;

EID: 0036210883     PISSN: 00219193     EISSN: None     Source Type: Journal    
DOI: 10.1128/JB.184.8.2072-2080.2002     Document Type: Article

References (47)

1. Gapped BLAST and PSI-BLAST: A new generation of protein database search programs
2. Evidence for massive gene exchange between archaeal and bacterial hyperthermophiles
3. Reply
4. Automated pair-wise comparisons of microbial genomes
5. Perspectives on archaeal diversity, thermophily and monophyly from environmental rRNA sequences
6. Evolutionary origins of the haloarchaeal genome
7. Archaea: Whose sister lineage?
8. Phylogenetic classification and the universal tree
9. Uprooting the tree of life
10. Molecular interactions in extreme halophiles - The solvation-stabilization hypothesis for halophilic proteins
11. PHYLIP - Phylogeny inference package (version 3.2)
12. Confidence limits on phylogenies: An approach using the bootstrap
13. Distinguishing homologous from analogous proteins
14. Whole genome-based phylogenetic analysis of free-living microorganisms
15. Compositional bias may affect both DNA-based and protein-based phylogenetic reconstructions
16. Horizontal gene transfer in bacterial and archaeal complete genomes
17. From complete genomes to measures of substitution rate variability within and between proteins
18. Measuring genome evolution
19. Horizontal gene transfer among genomes: The complexity hypothesis
20. Prokaryotic genomes: The emerging paradigm of genome-based microbiology
21. Comparison of archaeal and bacterial genomes: Computer analysis of protein sequences predicts novel functions and suggests a chimeric origin for the archaea
22. The closest BLAST hit is often not the nearest neighbor
23. Archaeal and bacterial hyperthermophiles. Horizontal gene exchange or common ancestry?
24. Amelioration of bacterial genomes: Rates of change and exchange
25. Reconciling the many faces of lateral gene transfer
26. Genomic flux: Genome evolution by gene loss and acquisition
27. Whole-genome trees based on the occurrence of folds and orthologs: Implications for comparing genomes on different levels
28. Evolutionary genomics: Thermotoga heats up lateral gene transfer
29. The RDP-II (Ribosomal Database Project)
30. A minimal gene set for cellular life derived by comparison of complete bacterial genomes
31. Evidence for lateral gene transfer between archaea and bacteria from genome sequence of Thermotoga maritima
32. Lateral gene transfer and the nature of bacterial innovation
33. The winds of (evolutionary) change: Breathing new life into microbiology
34. A molecular view of microbial diversity and the biosphere
35. TREEVIEW: An application to display phylogenetic trees on personal computers
36. Detection of lateral gene transfer among microbial genomes
37. Distributional profiles of homologous open reading frames among bacterial phyla: Implications for vertical and lateral transmission
38. Diversity of radA genes from cultured and uncultured Archaea: Comparative analysis of putative RadA proteins and their use as a phylogenetic marker
39. Genome phylogeny based on gene content
40. The genomic tree as revealed from whole proteome comparisons
41. Interpreting the universal phylogenetic tree
42. Genome trees constructed using five different approaches suggest new major bacterial clades
43. Jackknife, bootstrap and other resampling methods in regression analysis
44. Evolutionary divergence and convergence in proteins