© 2007 Society of Systematic Biologists
Improvement of Phylogenies after Removing Divergent and Ambiguously Aligned Blocks from Protein Sequence Alignments
1 Department of Physiology and Molecular Biodiversity, Institute of Molecular Biology of Barcelona CSIC, Jordi Girona 18, Barcelona, 08034, Spain E-mail: jcvagr{at}ibmb.csic.es (J.C.)
Edited by Karl Kjer: Associate Editor Rod Page Editor Jack Sullivan Editor
 |
Abstract |
|---|
Alignment quality may have as much impact on phylogenetic reconstruction as the phylogenetic methods used. Not only the alignment algorithm, but also the method used to deal with the most problematic alignment regions, may have a critical effect on the final tree. Although some authors remove such problematic regions, either manually or using automatic methods, in order to improve phylogenetic performance, others prefer to keep such regions to avoid losing any information. Our aim in the present work was to examine whether phylogenetic reconstruction improves after alignment cleaning or not. Using simulated protein alignments with gaps, we tested the relative performance in diverse phylogenetic analyses of the whole alignments versus the alignments with problematic regions removed with our previously developed Gblocks program. We also tested the performance of more or less stringent conditions in the selection of blocks. Alignments constructed with different alignment methods (ClustalW, Mafft, and Probcons) were used to estimate phylogenetic trees by maximum likelihood, neighbor joining, and parsimony. We show that, in most alignment conditions, and for alignments that are not too short, removal of blocks leads to better trees. That is, despite losing some information, there is an increase in the actual phylogenetic signal. Overall, the best trees are obtained by maximum-likelihood reconstruction of alignments cleaned by Gblocks. In general, a relaxed selection of blocks is better for short alignment, whereas a stringent selection is more adequate for longer ones. Finally, we show that cleaned alignments produce better topologies although, paradoxically, with lower bootstrap. This indicates that divergent and problematic alignment regions may lead, when present, to apparently better supported although, in fact, more biased topologies.
Keywords: Bootstrap support; Gblocks; phylogeny; sequence alignment
Received February 7, 2007; Revised March 6, 2007; Accepted March 24, 2007
CiteULike 
Connotea 
Del.icio.us What's this?
This article has been cited by other articles:
|
|
 |
|
  S. Cook, G. Moureau, R. E. Harbach, L. Mukwaya, K. Goodger, F. Ssenfuka, E. Gould, E. C. Holmes, and X. de Lamballerie Isolation of a novel species of flavivirus and a new strain of Culex flavivirus (Flaviviridae) from a natural mosquito population in Uganda J. Gen. Virol., November 1, 2009; 90(11): 2669 - 2678. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 B. Pils and A. Heyl Unraveling the Evolution of Cytokinin Signaling Plant Physiology, October 1, 2009; 151(2): 782 - 791. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 L. S. Haggerty, F. J. Martin, D. A. Fitzpatrick, and J. O. McInerney Gene and genome trees conflict at many levels Phil Trans R Soc B, August 12, 2009; 364(1527): 2209 - 2219. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 S. Capella-Gutierrez, J. M. Silla-Martinez, and T. Gabaldon trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses Bioinformatics, August 1, 2009; 25(15): 1972 - 1973. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 B. Misof and K. Misof A Monte Carlo Approach Successfully Identifies Randomness in Multiple Sequence Alignments: A More Objective Means of Data Exclusion Syst Biol, May 20, 2009; (2009) syp006v1. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 S. Schelbert, S. Aubry, B. Burla, B. Agne, F. Kessler, K. Krupinska, and S. Hortensteiner Pheophytin Pheophorbide Hydrolase (Pheophytinase) Is Involved in Chlorophyll Breakdown during Leaf Senescence in Arabidopsis PLANT CELL, March 1, 2009; 21(3): 767 - 785. [Abstract] [Full Text] [PDF]
|
|