Accounting For Alignment Uncertainty in Phylogenomics

@inproceedings{Wu2012AccountingFA,
  title={Accounting For Alignment Uncertainty in Phylogenomics},
  author={Martin Wu and Sourav Chatterji and Jonathan A. Eisen},
  booktitle={PloS one},
  year={2012}
}
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… CONTINUE READING
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