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Updated: May 25, 2026

Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin
Published on: August 14, 2018
Accounting for alignment uncertainty in phylogenomics
Martin Wu1, Sourav Chatterji, Jonathan A Eisen
1Department 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.
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