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Accounting For Alignment Uncertainty in Phylogenomics

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  • Martin Wu
  • Sourav Chatterji
  • Jonathan A Eisen

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.

Suggested Citation

  • Martin Wu & Sourav Chatterji & Jonathan A Eisen, 2012. "Accounting For Alignment Uncertainty in Phylogenomics," PLOS ONE, Public Library of Science, vol. 7(1), pages 1-10, January.
    • Handle: RePEc:plo:pone00:0030288
    DOI: 10.1371/journal.pone.0030288
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    1. José Cerca & Bent Petersen & José Miguel Lazaro-Guevara & Angel Rivera-Colón & Siri Birkeland & Joel Vizueta & Siyu Li & Qionghou Li & João Loureiro & Chatchai Kosawang & Patricia Jaramillo Díaz & Gon, 2022. "The genomic basis of the plant island syndrome in Darwin’s giant daisies," Nature Communications, Nature, vol. 13(1), pages 1-13, December.

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