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indelible website  

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.

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 modelled via the continuous and discrete gamma distributions, with or without a proportion of invariant sites. INDELible can also simulate under non-homogenous and non-stationary conditions where evolutionary models are permitted to change across a phylogeny.

Environment Modules

Run module spider indelible to find out what environment modules are available for this application.

System Variables

  • HPC_INDELIBLE_DIR - installation directory
  • HPC_INDELIBLE_BIN - executable directory


If you publish research that uses indelible you have to cite it as follows:

Fletcher, W. and Yang, Z. 2009. INDELible: a flexible simulator of biological sequence evolution. Mol. Biol. and Evol. 2009 26(8):1879-1888