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INDELible: A Flexible Simulator of Biological Sequence Evolution William Fletcher and Ziheng Yang

Summary: INDELible: A Flexible Simulator of Biological Sequence Evolution
William Fletcher and Ziheng Yang
Department of Genetics, Evolution and Environment and Centre for Mathematics and Physics in the Life Sciences and Experimental
Biology, University College London, London, United Kingdom
Many methods exist for reconstructing phylogenies from molecular sequence data, but few phylogenies are known and
can be used to check their efficacy. Simulation remains the most important approach to testing the accuracy and
robustness of phylogenetic inference methods. However, current simulation programs are limited, especially concerning
realistic models for simulating insertions and deletions. We implement a portable and flexible application, named
INDELible, for generating nucleotide, amino acid and codon sequence data by simulating insertions and deletions
(indels) as well as substitutions. Indels are simulated under several models of indel-length distribution. The program
implements a rich repertoire of substitution models, including the general unrestricted model and nonstationary
nonhomogeneous models of nucleotide substitution, mixture, and partition models that account for heterogeneity among
sites, and codon models that allow the nonsynonymous/synonymous substitution rate ratio to vary among sites and
branches. With its many unique features, INDELible should be useful for evaluating the performance of many inference
methods, including those for multiple sequence alignment, phylogenetic tree inference, and ancestral sequence, or
genome reconstruction.
A variety of methods and computer programs are avail-
able for aligning multiple sequences, reconstructing phyloge-
netic trees, and estimating evolutionary parameters. Because


Source: Anisimova, Maria - Institute of Scientific Computing, Eidgenössische Technische Hochschule Zürich (ETHZ)
Yang, Ziheng - Department of Genetics, Evolution and Environment, University College London


Collections: Biology and Medicine; Environmental Sciences and Ecology