There are a number of tools but I don't know any that comes with an R library. They are usually all called from the command line. I don't either of any that produce FASTA file. [SimBit][1] (my own software) can produce `vcf` files which can easily be converted into FASTA with PGDspider

However, if your simulations are so easy, you might not need these complex individual-based softwares. Just write the code yourself. It might only be take a few tens of lines. Here is a simple example

    for (generation in 1:nbGenerations)
    {
       # Drift
       freq = rbinom(1,N,freq) / N
    
       # Mutations
       oneWayMutations   = rbinom(1,N*freq,mu) / N
       otherWayMutations = rbinom(1,N*(1-freq),mu) / N
       freq = freq - oneWayMutations + otherWayMutations
    }

  [1]: https://github.com/RemiMattheyDoret/SimBit