I have fasta sequences of a virus protein that had suffered a mutation in 2008 and this mutant had increase it fitness when compared to wild strain (according to literature).I want to simulate if my sequences were submitted in 2009(I have sequences from 2009 and 2010) or before to mutation and simulate next sequences to verify if the population of mutants really turns majority. How can I do that?My virus is a RNA -ss. Any tool to use that i can represent it graphically? Or simplifying..I want to simulate the past and the future sequences of my dataset.


From the description of the model you are interested in, you probably don't need numerical simulations. A simple analytical expectation might be enough. But anyway, if you want to perform numerical simulations (maybe you don't want to assume panmixia), then there are a number of choices to you.

The simulator that you will need needs to be able to implement selection. It hence need to be a forward-in-time simulator and not a coalescent simulator. I personally have experienced with 4 different forward-in-time simulators; SimBit, SLiM, SFS_code and Nemo.

If I am not mistaken, SFS_code won't be able to simulate haploid individuals and will probably be slower than SimBit and SLiM. In SimBit, SLiM and Nemo you cannot do haploid either, however, you can set the cloning rate to 100%, which will essentially be the same as simulating haploids.

To my experience and generally speaking, SLiM and SimBit are faster than Nemo. Because your mutation rate is high and because your recombination rate will be very low (will probably be zero), SimBit should be very very fast and SLiM relatively slow. Also, SimBit will offer much nicer outputs for the statistic you are interested in than SLiM does.

Please note that I am the author of SimBit and I therefore might have a conflict of interest here. Here is the link to SimBit.


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