Inferring Indel Parameters using a Simulation-based Approach.
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ABSTRACT:
SUBMITTER: Levy Karin E
PROVIDER: S-EPMC4700945 | biostudies-literature | 2015 Nov
REPOSITORIES: biostudies-literature
Publications
Inferring Indel Parameters using a Simulation-based Approach.
Levy Karin Eli E Rabin Avigayel A Ashkenazy Haim H Shkedy Dafna D Avram Oren O Cartwright Reed A RA Pupko Tal T
Genome biology and evolution 20151103 12
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 par ...[more]
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