Hi all,
I have a potentially hard ask, but I have been unable to find anything myself so I'm hoping that someone might know of a program that can do what I'm looking for.
I'm looking to see if there is a program where I can input a single sequence file, give it a model of nucleotide evolution, then evolve it forward in time over x number of years or generation.
Different to simulating sequence evolution, I am only looking to evolve one sequence forward in time, by which I mean that it has no descendants, just one sequence that continues to mutate over time. This also means that it cannot dependent on a tree. I also need to be able to give it a sequence file as an input, as I would run this multiple times, and need to have an identical starting sequence.
Thanks in advance,
Tim
There are several programs that do this. Most will select many "children" in the generations, but you can just discard all but one.
http://bioinformatics.org/spower/simseq
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2612967/
https://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-12-104
Hi Brian,
Thank you for taking the time to reply and providing links, it is much appreciated. I've had a look through the links your provided, and unfortunately it is not quite what I am looking for, as I am looking for a method that allows me to specify a real sequence as the starting sequence.
Thank you for your help regardless,
Tim
It seems difficult to believe that what you are looking for is so hard to find. I found the following site: https://popmodels.cancercontrol.cancer.gov/gsr/packages/ genetic simulation resources and even there I am not sure any of them does what you are asking. I would recommend writing to the authors of one of the packages that comes close to doing what you want, to ask them if they know the solution.
Hi Brian,
Thank you for your help in this! I may have actually found a solution when reading through the literature you originally sent me. Seq-Gen (http://tree.bio.ed.ac.uk/software/seqgen/) allows you to input a number of sequences, and choose amongst them your ancestral sequence. In addition to this, if you specify the seed number, then "Seq-Gen will generate exactly the same simulated data. Thus by recording the options and seed, it is possible to regenerate a simulated data set".
While it does rely on a tree, similar to what you said earlier in regards to only selecting one child per generation, I can simulate the evolution of this one sequence along a tree with a single branch!
I'm just playing with this software now, I'll let you know how I go. Thanks again, Brain!
Cheers,
Tim
Article SEQ-GEN: An application for the Monte Carlo simulation of DN...
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