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Phylogenetic assessment of alignments reveals neglected tree signal in gaps

Christophe Dessimoz12* and Manuel Gil12

Author Affiliations

1 Department of Computer Science, ETH Zurich, Universitaetstr. 6, 8092 Zürich, Switzerland

2 Swiss Institute of Bioinformatics, Universitaetstr. 6, 8092 Zurich, Switzerland

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Genome Biology 2010, 11:R37  doi:10.1186/gb-2010-11-4-r37

Published: 6 April 2010



The alignment of biological sequences is of chief importance to most evolutionary and comparative genomics studies, yet the two main approaches used to assess alignment accuracy have flaws: reference alignments are derived from the biased sample of proteins with known structure, and simulated data lack realism.


Here, we introduce tree-based tests of alignment accuracy, which not only use large and representative samples of real biological data, but also enable the evaluation of the effect of gap placement on phylogenetic inference. We show that (i) the current belief that consistency-based alignments outperform scoring matrix-based alignments is misguided; (ii) gaps carry substantial phylogenetic signal, but are poorly exploited by most alignment and tree building programs; (iii) even so, excluding gaps and variable regions is detrimental; (iv) disagreement among alignment programs says little about the accuracy of resulting trees.


This study provides the broad community relying on sequence alignment with important practical recommendations, sets superior standards for assessing alignment accuracy, and paves the way for the development of phylogenetic inference methods of significantly higher resolution.