Accounting for alignment uncertainty in phylogenomics.
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ABSTRACT:
SUBMITTER: Wu M
PROVIDER: S-EPMC3260272 | biostudies-literature | 2012
REPOSITORIES: biostudies-literature
Publications
Accounting for alignment uncertainty in phylogenomics.
Wu Martin M Chatterji Sourav S Eisen Jonathan A JA
PloS one 20120117 1
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 signi ...[more]
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