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.