Skip Navigation

This Article
Right arrow Full Text Freely available
Right arrow FREE Full Text (PDF) Freely available
Right arrow Alert me when this article is cited
Right arrow Alert me if a correction is posted
Services
Right arrow Email this article to a friend
Right arrow Similar articles in this journal
Right arrow Similar articles in ISI Web of Science
Right arrow Similar articles in PubMed
Right arrow Alert me to new issues of the journal
Right arrow Add to My Personal Archive
Right arrow Download to citation manager
Right arrow Search for citing articles in:
ISI Web of Science (20)
Right arrowRequest Permissions
Google Scholar
Right arrow Articles by Ranwez, V.
Right arrow Articles by Gascuel, O.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Ranwez, V.
Right arrow Articles by Gascuel, O.
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us  
What's this?

Molecular Biology and Evolution 18:1103-1116 (2001)
© 2001 Society for Molecular Biology and Evolution

Quartet-Based Phylogenetic Inference: Improvements and Limits

Vincent Ranwez and Olivier Gascuel

Département Informatique Fondamentale et Applications, Montpellier, France

We analyze the performance of quartet methods in phylogenetic reconstruction. These methods first compute four-taxon trees (4-trees) and then use a combinatorial algorithm to infer a phylogeny that respects the inferred 4-trees as much as possible. Quartet puzzling (QP) is one of the few methods able to take weighting of the 4-trees, which is inferred by maximum likelihood, into account. QP seems to be widely used. We present weight optimization (WO), a new algorithm which is also based on weighted 4-trees. WO is faster and offers better theoretical guarantees than QP. Moreover, computer simulations indicate that the topological accuracy of WO is less dependent on the shape of the correct tree. However, although the performance of WO is better overall than that of QP, it is still less efficient than traditional phylogenetic reconstruction approaches based on pairwise evolutionary distances or maximum likelihood. This is likely related to long-branch attraction, a phenomenon to which quartet methods are very sensitive, and to inappropriate use of the initial results (weights) obtained by maximum likelihood for every quartet.


Add to CiteULike CiteULike   Add to Connotea Connotea   Add to Del.icio.us Del.icio.us    What's this?


This article has been cited by other articles:


Home page
 Syst BiolHome page
R. C. Winkworth, D. Bryant, P. J. Lockhart, D. Havell, and V. Moulton
Biogeographic Interpretation of Splits Graphs: Least Squares Optimization of Branch Lengths
Syst Biol, February 1, 2005; 54(1): 56 - 65.
[Abstract] [Full Text] [PDF]

Home page
 Syst BiolHome page
B. R. Holland, F. Delsuc, V. Moulton, and A. Baker
Visualizing Conflicting Evolutionary Hypotheses in Large Collections of Trees: Using Consensus Networks to Study the Origins of Placentals and Hexapods
Syst Biol, February 1, 2005; 54(1): 66 - 76.
[Abstract] [Full Text] [PDF]

Home page
 Mol Biol EvolHome page
L. S. Vinh and A. von Haeseler
IQPNNI: Moving Fast Through Tree Space and Stopping in Time
Mol. Biol. Evol., August 1, 2004; 21(8): 1565 - 1571.
[Abstract] [Full Text] [PDF]

Home page
 Proc. Natl. Acad. Sci. USAHome page
H. Brinkmann, B. Venkatesh, S. Brenner, and A. Meyer
Nuclear protein-coding genes support lungfish and not the coelacanth as the closest living relatives of land vertebrates
PNAS, April 6, 2004; 101(14): 4900 - 4905.
[Abstract] [Full Text] [PDF]

Home page
 Mol Biol EvolHome page
V. Ranwez and O. Gascuel
Improvement of Distance-Based Phylogenetic Methods by a Local Maximum Likelihood Approach Using Triplets
Mol. Biol. Evol., November 1, 2002; 19(11): 1952 - 1963.
[Abstract] [Full Text] [PDF]

Home page
 J. Cell Sci.Home page
J. B. Dacks and W. F. Doolittle
Novel syntaxin gene sequences from Giardia, Trypanosoma and algae: implications for the ancient evolution of the eukaryotic endomembrane system
J. Cell Sci., April 15, 2002; 115(8): 1635 - 1642.
[Abstract] [Full Text] [PDF]


Disclaimer: Please note that abstracts for content published before 1996 were created through digital scanning and may therefore not exactly replicate the text of the original print issues. All efforts have been made to ensure accuracy, but the Publisher will not be held responsible for any remaining inaccuracies. If you require any further clarification, please contact our Customer Services Department.