TAILIEUCHUNG - Accounting For Alignment Uncertainty in Phylogenomics

International standards are not necessarily appropriate to govern all financial reporting obligations, this being especially the case with International Accounting Standards (IAS) / International Financial Reporting Standards (IFRS). There is an urgent need for the International Accounting Standards Board to specify the circumstances in which the use of “full” IAS/IFRS is appropriate, and to develop different standards that would meet the needs applicable to the users of financial statements of other entities, particularly small and medium-sized enterprises (SMEs). Many stakeholders continue to have misunderstandings with respect to the very nature of international standards, which complicates efforts to plan, define. | OPEN 3 ACCESS Freely available online PLosone Accounting For Alignment Uncertainty in Phylogenomics Martin Wu1 . Sourav Chatterji2 Jonathan A. Eisen2 3 4 1 Department of Biology University of Virginia Charlottesville Virginia United States ofAmerica 2 Genome Center University ofCalifornia Davis California United States of America 3 Section of Evolution and Ecology College of Biological Sciences University of California Davis California United States ofAmerica 4 Department of Medical Microbiology and Immunology School of Medicine University of California Davis California United States of America 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. Citation Wu M Chatterji S Eisen JA 2012 Accounting For Alignment Uncertainty in Phylogenomics. PLoS ONE 7 1 e30288. doi Editor Marco Salemi University of Florida United States of America Received October 8 2011 Accepted December 14 2011 Published January 17 2012 Copyright 2012 Wu et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License which permits unrestricted use distribution and reproduction in any medium provided the original author and source are credited. Funding This was supported by Grant 1660 from the Gordon and Betty Moore Foundation. The funders had no role in study design data collection and analysis decision to publish or preparation of the manuscript. Competing Interests The authors have declared that no .

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