Is there a program that can take a simple fasta file representing a genomic locus and add mutations including indels? Ideally, we are looking for a program can where we can specify different rates of mutation for different coordinates as well as the transition to transversion ratio.
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Gabriel R.
See if SimuG might work for your needs:
A simple, flexible, and powerful tool to simulate genome sequences with pre-defined or random genomic variants.
thank you for the message! I had a look at it, it does not seem to be able to simulate a mutation rate rather than a number of SNPs. Also, it does not allow different mutations rate correct?
I have not used it sufficiently to know of all of its features, but it does take a large number of parameters and it can do:
For random variants, simuG supports a wide-spectrum of fine control options, such as ‘-titv_ratio’ for specifying the transition/transversion ratio of SNPs,
and
For each variant type, simuG can simulate pre-defined or random variants depending on specified options.
I would explore it more, then look for citations to this tool via PubMed to explore newer options
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