indel-Seq-Gen (iSG) is a biological sequence simulation program that simulates highly divergent DNA sequences and protein superfamilies. This is accomplished through the addition of subsequence length constraints and lineage- and site-specific evolution. iSG tracks insertion and deletion processes that occur during the simulation run. iSG records all evolutionary events and outputs the “true” multiple alignment of the sequences, and can generate a larger simulated sequence space by allowing the use of multiple related root sequences. iSG can be used to test the accuracy of multiple alignment methods, evolutionary hypotheses, ancestral protein reconstruction methods, and protein superfamily classification methods.
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Biological sequence simulation for testing complex evolutionary hypotheses: indel-Seq-Gen version 2.0.
Strope CL, Abel K, Scott SD, Moriyama EN.
Mol Biol Evol. 2009 Nov;26(11):2581-93. doi: 10.1093/molbev/msp174.