Accounting for alignment uncertainty in phylogenomics

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


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.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Algorithms
  • Amino Acid Sequence
  • Animals
  • Computational Biology / methods*
  • Evolution, Molecular
  • Genomics / methods
  • Humans
  • Phylogeny*
  • Reproducibility of Results
  • Sequence Alignment / methods*
  • Software*
  • Uncertainty