INDELible is a new, portable, and flexible application for biological
sequence simulation that combines many features in the same place for
the first time. Using a length-dependent model of indel formation it
can simulate evolution of multi-partitioned nucleotide, amino-acid,
or codon data sets through the processes of insertion, deletion, and
substitution in continuous time.
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Nucleotide simulations may use the general unrestricted model or the
general time reversible model and its derivatives, and amino-acid
simulations can be conducted using fifteen different empirical rate
matrices. Substitution rate heterogeneity can be modeled via the
continuous and discrete gamma distributions, with or without a proportion
of invariant sites. INDELible can also simulate under non-homogeneous
and non-stationary conditions where evolutionary models are permitted
to change across a phylogeny.
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Unique among indel simulation programs, INDELible offers the ability
to simulate using codon models that exhibit nonsynonymous/synonymous
rate ratio heterogeneity among sites and/or lineages.
