title: Indel reliability in indel-based phylogenetic inference.
abstract: It is often assumed that it is unlikely that the same insertion or deletion (indel) event occurred at the same position in two independent evolutionary lineages, and thus, indel-based inference of phylogeny should be less subject to homoplasy compared with standard inference which is based on substitution events. Indeed, indels were successfully used to solve debated evolutionary relationships among various taxonomical groups. However, indels are never directly observed but rather inferred from the alignment and thus indel-based inference may be sensitive to alignment errors. It is hypothesized that phylogenetic reconstruction would be more accurate if it relied only on a subset of reliable indels instead of the entire indel data. Here, we developed a method to quantify the reliability of indel characters by measuring how often they appear in a set of alternative multiple sequence alignments. Our approach is based on the assumption that indels that are consistently present in most alternative alignments are more reliable compared with indels that appear only in a small subset of these alignments. Using simulated and empirical data, we studied the impact of filtering and weighting indels by their reliability scores on the accuracy of indel-based phylogenetic reconstruction. The new method is available as a web-server at http://guidance.tau.ac.il/RELINDEL/.
authors.affiliation: Department of Cell Research and Immunology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Ramat Aviv, Israel.
authors.forename: Haim
authors.initials: H
authors.lastname: Ashkenazy
authors.affiliation: Department of Cell Research and Immunology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Ramat Aviv, Israel Present address: Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel.
authors.forename: Ofir
authors.initials: O
authors.lastname: Cohen
authors.affiliation: Department of Cell Research and Immunology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Ramat Aviv, Israel talp@post.tau.ac.il huchond@post.tau.ac.il.
authors.forename: Tal
authors.initials: T
authors.lastname: Pupko
authors.affiliation: Department of Zoology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Ramat Aviv, Israel talp@post.tau.ac.il huchond@post.tau.ac.il.
authors.forename: Dorothée
authors.initials: D
authors.lastname: Huchon
mesh_terms: D000818:Animals; D019143:Evolution, Molecular; D006801:Humans; D054643:INDEL Mutation; D010802:Phylogeny; D012680:Sensitivity and Specificity; D016415:Sequence Alignment / Q000379:methods*; D012984:Software
keywords: alignment reliability; indel analysis; multiple sequence alignment; phylogeny