ArticlePloS one2012
Accounting for alignment uncertainty in phylogenomics.
Article in PloS one, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 100 papers.
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100 citing papers in PubMed.
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- PhyloBench: A Benchmark for Evaluating Phylogenetic Programs.Molecular biology and evolution · 2024Article
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- Mito-nuclear coevolution and phylogenetic artifacts: the case of bivalve mollusks.Scientific reports · 2022Article
- The genomic basis of the plant island syndrome in Darwin's giant daisies.Nature communications · 2022Article
- Phylogenies from unaligned proteomes using sequence environments of amino acid residues.Scientific reports · 2022Article
- The First Genome of the Balearic Shearwater (Puffinus mauretanicus) Provides a Valuable Resource for Conservation Genomics and Sheds Light on Adaptation to a Pelagic lifestyle.Genome biology and evolution · 2022Article
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- Phylogenomic Analysis of Velvet Worms (Onychophora) Uncovers an Evolutionary Radiation in the Neotropics.Molecular biology and evolution · 2021Article
- Faster Rates of Molecular Sequence Evolution in Reproduction-Related Genes and in Species with Hypodermic Sperm Morphologies.Molecular biology and evolution · 2021Article
- A comprehensive synthesis unveils the mysteries of phosphate-solubilizing microbes.Biological reviews of the Cambridge Philosophical Society · 2021Article
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40 more citing papers are in PubMed but not listed here.
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3 authors.
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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.
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