title: Inferring Indel Parameters using a Simulation-based Approach.
abstract: In this study, we present a novel methodology to infer indel parameters from multiple sequence alignments (MSAs) based on simulations. Our algorithm searches for the set of evolutionary parameters describing indel dynamics which best fits a given input MSA. In each step of the search, we use parametric bootstraps and the Mahalanobis distance to estimate how well a proposed set of parameters fits input data. Using simulations, we demonstrate that our methodology can accurately infer the indel parameters for a large variety of plausible settings. Moreover, using our methodology, we show that indel parameters substantially vary between three genomic data sets: Mammals, bacteria, and retroviruses. Finally, we demonstrate how our methodology can be used to simulate MSAs based on indel parameters inferred from real data sets.
authors.affiliation: Department of Cell Research and Immunology, George S. Wise Faculty of Life Sciences, Tel-Aviv University, Tel-Aviv, Israel.
authors.forename: Eli
authors.initials: E
authors.lastname: Levy Karin
authors.affiliation: Department of Cell Research and Immunology, George S. Wise Faculty of Life Sciences, Tel-Aviv University, Tel-Aviv, Israel.
authors.forename: Avigayel
authors.initials: A
authors.lastname: Rabin
authors.affiliation: Department of Cell Research and Immunology, George S. Wise Faculty of Life Sciences, Tel-Aviv University, Tel-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, Tel-Aviv, Israel.
authors.forename: Dafna
authors.initials: D
authors.lastname: Shkedy
authors.affiliation: Department of Cell Research and Immunology, George S. Wise Faculty of Life Sciences, Tel-Aviv University, Tel-Aviv, Israel The Blavatnik School of Computer Science, Tel-Aviv University, Tel-Aviv, Israel.
authors.forename: Oren
authors.initials: O
authors.lastname: Avram
authors.affiliation: The Biodesign Institute, Arizona State University, Tempe School of Life Sciences, Arizona State University, Tempe.
authors.forename: Reed A
authors.initials: RA
authors.lastname: Cartwright
authors.affiliation: Department of Cell Research and Immunology, George S. Wise Faculty of Life Sciences, Tel-Aviv University, Tel-Aviv, Israel talp@post.tau.ac.il.
authors.forename: Tal
authors.initials: T
authors.lastname: Pupko
mesh_terms: D000818:Animals; D016680:Genome, Bacterial; D016679:Genome, Viral; D054643:INDEL Mutation; D008322:Mammals; D016415:Sequence Alignment / Q000379:methods*; D012984:Software
keywords: Mahalanobis distance; alignments; indels; phylogeny; simulations