Inferring Rates and Length-Distributions of Indels Using Approximate Bayesian Computation.

ABSTRACT: The most common evolutionary events at the molecular level are single-base substitutions, as well as insertions and deletions (indels) of short DNA segments. A large body of research has been devoted to develop probabilistic substitution models and to infer their parameters using likelihood and Bayesian approaches. In contrast, relatively little has been done to model indel dynamics, probably due to the difficulty in writing explicit likelihood functions. Here, we contribute to the effort of modeling indel dynamics by presenting SpartaABC, an approximate Bayesian computation (ABC) approach to infer indel parameters from sequence data (either aligned or unaligned). SpartaABC circumvents the need to use an explicit likelihood function by extracting summary statistics from simulated sequences

SUBMITTER: Levy Karin E 

PROVIDER: S-EPMC5438127 | biostudies-literature | 2017 May

REPOSITORIES: biostudies-literature