Quartet puzzling: A quartet maximum-likelihood method for reconstructing tree topologies

Molecular Biology and Evolution

Volumn 13, Issue 7, 1996, Pages 964-969

  Strimmer, Korbinian ^a   Von Haeseler, Arndt ^a  

^a UNIVERSITY OF MUNICH   (Germany)

Author keywords

bootstrapping; consensus tree; maximum likelihood; quartet puzzling; quartet trees; reliability of internal branches; tree reconstruction

Indexed keywords

AMINO ACID; DNA; MITOCHONDRIAL RNA; TRANSFER RNA;

ACCURACY; AMINO ACID SEQUENCE; ARTICLE; DNA SEQUENCE; EVOLUTION; PHYLOGENY; TECHNIQUE;

AMNIOTA;

EID: 0029836454     PISSN: 07374038     EISSN: None     Source Type: Journal    
DOI: 10.1093/oxfordjournals.molbev.a025664     Document Type: Article

References (21)

1. ADACHI, J, and M. HASEGAWA, 1994. MOLPHY: programs for molecular phylogenetics. Version 2.2. Institute of Statistical Mathematics, Tokyo.
2. BANDELT, H.-J., and A. DRESS. 1986. Reconstructing the shape of a tree from observed dissimilarity data. Adv. Appl. Math. 7:309-343.
3. DRESS, A., A. VON HAESELER, and M. KRÜGER. 1986. Reconstructing phylogenetic tress using variants of the four-point condition. Studien zur Klassifikation 17:299-305.
4. FELSENSTEIN, J. 1981. Evolutionary trees from DNA sequences: a maximum likelihood approach. J. Mol. Evol. 17:368-376.
5. _. 1988. Phylogenies from molecular sequences: inference and reliability. Annu. Rev. Genet. 22:521-565.
6. _. 1993. PHYLIP: phylogenetic inference package. Version. 3.5c. Department of Genetics, University of Washington, Seattle.
7. FITCH, W. M. 1981. A non-sequential method for constructing trees and hierarchical classifications. J. Mol. Evol. 18:30-37.
8. HASEGAWA, M., H. KISHINO, and K. YANO. 1985. Dating of the human-ape splitting by a molecular clock of mitochondrial DNA. J. Mol. Evol. 22:160-174.
9. HEDGES, S. B. 1994. Molecular evidence for the origin of birds Proc. Natl. Acad. Sci. USA 91:2621-2624.
10. JANKE, A., G. FELDMAIER-FUCHS, N. GEMMELL, A. VON HAESELER, and S. PAÄBO. 1996. The complete mitochondrial genome of the platypus (Ornithorhynchus anatinus) and the evolution of mammals. J. Mol. Evol. 42:153-159.
11. JANKE, A., G. FELDMAIER-FUCHS, W. K. THOMAS, A. VON HAESELER, and S. PÄÄBO. 1994. The marsupial mitochondrial genome and the evolution of placental mammals. Genetics 137:243-256.
12. JUKES, T. H., and C. R CANTOR. 1969. Evolution of protein molecules. Pp. 21-132 in H. N. MUNRO, ed. Mammalian protein metabolism. Academic Press, New York.
13. KIMURA, M. 1980. A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J. Mol. Evol. 16:111-120.
14. MARGUSH, T., and F. R. MCMORRIS. 1981. Consensus n-trees. Bull. Math. Biol. 43:239-244.
15. OLSEN, G. J., H. NATSUDA, R. HAGSTROM, and R. OVERBEEK. 1994. FastDNAML: a tool for construction of phylogenetic trees of DNA sequences using maximum likelihood. CABIOS 10:41-48.
16. PENNY, D., M. STEEL, P. J. WADDELL, and M. D. HENDY. 1995. Improved analyses of human mtDNA sequences support a recent African origin of Homo sapiens. Mol. Biol. Evol. 12: 863-882.
17. SAITOU, N., and M. NEI. 1987. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol. Biol. Evol. 4:406-425.
18. SATTATH, S., and A. TVERSKY. 1977. Additive similarity trees. Psychometrika 42:319-345.
19. SCHÖNIGER, M., and A. VON HAESELER. 1993. A simple method to improve the reliability of tree reconstructions. Mol. Biol. Evol. 10:471-483.
20. THOMPSON, J. D., D. G. HIGGINS, and T. J. GIBSON. 1994. CLUSTAL W: improving the sensitivity of progressive multiple alignment through sequence weighting, positions-specific gap penalties and weight matrix choice. Nucleic Acids Res. 22:4673-4680.
21. YANG, Z. 1995. Phylogenetic Analysis by maximum likelihood (PAML). Version 1.1. Institute of Molecular Evolutionary Genetics, Pennsylvania State University, University Park, Pa.