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PLoS One. 2012;7(1):e30288. doi: 10.1371/journal.pone.0030288. Epub 2012 Jan 17.

Accounting for alignment uncertainty in phylogenomics.

Author information

1
Department of Biology, University of Virginia, Charlottesville, Virginia, United States of America. mw4yv@virginia.edu

Abstract

Uncertainty in multiple sequence alignments has a large impact on phylogenetic analyses. Little has been done to evaluate the quality of individual positions in protein sequence alignments, which directly impact the accuracy of phylogenetic trees. Here we describe ZORRO, a probabilistic masking program that accounts for alignment uncertainty by assigning confidence scores to each alignment position. Using the BALIBASE database and in simulation studies, we demonstrate that masking by ZORRO significantly reduces the alignment uncertainty and improves the tree accuracy.

PMID:
22272325
PMCID:
PMC3260272
DOI:
10.1371/journal.pone.0030288
[Indexed for MEDLINE]
Free PMC Article

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