Accounting for alignment uncertainty in phylogenomics

Martin Wu, Sourav Chatterji, Jonathan A Eisen

Research output: Contribution to journalArticlepeer-review

136 Scopus citations


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.

Original languageEnglish (US)
Article numbere30288
JournalPLoS One
Issue number1
StatePublished - Jan 17 2012

ASJC Scopus subject areas

  • Agricultural and Biological Sciences(all)
  • Biochemistry, Genetics and Molecular Biology(all)
  • Medicine(all)


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