Phylogeny for the faint of heart: A tutorial

Trends in Genetics

Volumn 19, Issue 6, 2003, Pages 345-351

  Baldauf, Sandra L ^a  

^a UNIVERSITY OF YORK   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

ANALYTIC METHOD; ARTIFACT; COMPUTER PROGRAM; LEARNING; LONG BRANCH ATTRACTION; NONHUMAN; PHYLOGENY; PLANT GENETICS; PLANT ROOT; PRIORITY JOURNAL; REVIEW; SEQUENCE HOMOLOGY; TREE;

EID: 0038204408     PISSN: 01689525     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0168-9525(03)00112-4     Document Type: Review

References (23)

1. Sneath P.H.A., Sokal R.R. Numerical Taxonomy. 1973;W.H. Freeman.
2. Zuckerkandl E., Pauling L. Evolutionary divergence and convergence in proteins. Bryson V., Vogel H.J. Evolving Genes and Proteins. 1965;97-166 Academic Press.
3. Iwabe N., et al. Evolutionary relationship of archaebacteria, eubacteria, and eukaryotes inferred from phylogenetic trees of duplicated genes. Proc. Natl. Acad. Sci. U. S. A. 86:1989;9355-9359.
4. +-ATPase: implications for the origin of eukaryotes. Proc. Natl. Acad. Sci. U. S. A. 86:1989;6661-6665.
5. Baldauf S.L., et al. The root of the universal tree and the origin of eukaryotes based on elongation factor phylogeny. Proc. Natl. Acad. Sci. U. S. A. 93:1996;7749-7754.
6. Boeckmann B., et al. The SWISS-PROT protein knowledgebase and its supplement TrEMBL in 2003. Nucleic Acids Res. 31:2003;365-370.
7. Altschul S.F., et al. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 25:1997;3389-3402.
8. Roberts L. A tussle over the rules for DNA data sharing. Science. 298:2003;1312-1313.
9. Schwartz R.M., Dayhoff M.O. Matrices for detecting distant relationships. Dayhoff M.O. Atlas of Protein Sequence and Structure. 1978;353-358 National Biomedical Research Foundation.
10. Feng D.F., Doolittle R.F. Progressive sequence alignment as a prerequisite to correct phylogenetic trees. J. Mol. Evol. 25:1987;351-360.
11. Higgins D.G., Sharp P.M. CLUSTAL: a package for performing multiple sequence alignment on a microcomputer. Gene. 73:1988;237-244.
12. Hall B.G. Phylogenetic Trees Made Easy: a How-To Manual for Molecular Biologists. 2000;Sinauer Associates.
13. Page R.D.M., Holmes E.C. Molecular Evolution: a Phylogenetic Approach. 1998;Blackwell Science.
14. Graur D., Li W.-H. Fundamentals of Molecular Evolution. 1999;Sinauer Associates.
15. Durbin R., et al. Biological Sequence Analysis. 2000;Cambridge University Press.
16. Nei M., Kumar S. Molecular Evolution and Phylogenetics. 2000;Cambridge University Press.
17. Swofford D.L., et al. Phylogenetic inference. Hillis D.M., et al. Molecular Systematics. 1996;Sinauer Associates.
18. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution. 39:1985;783-791.
19. Hillis D.M., Bull J.J. An empirical test of bootstrapping as a method for assessing confidence in phylogenetic analyses. Syst. Biol. 42:1993;182-192.
20. Felsenstein J. Cases in which parsimony or compatibility methods will be positively misleading. Syst. Zool. 27:1978;401-410.
21. Gribaldo S., Philippe H. Ancient phylogenetic relationships. Theor. Popul. Biol. 61:2002;391-408.
22. Hillis D.M., et al. Application and accuracy of molecular phylogenies. Science. 264:1994;671-677.
23. Zwickl D.J., Hillis D.M. Increased taxon sampling greatly reduces phylogenetic error. Syst Biol. 51:2002;588-598.