Is there a tool for synonymous recoding of DNA sequences? I've got a DNA sequence that I'd like to make synonymous mutations throughout, thereby preserving the amino acid sequence. Does anyone know of a tool to achieve this
There seems to be a bioconductor package named synmut which does just that.
Apparently, it can take codon usage into account when generating synonymous mutations.

Copy pasting an example that matches your use case from the official doc:

library("SynMut")
filepath.fasta &lt;- system.file("extdata", "example.fasta", package = "SynMut")
filepath.csv &lt;- system.file("extdata", "target_regions.csv", package = "SynMut")
region &lt;- read.csv(filepath.csv)
rgd.seq &lt;- input_seq(filepath.fasta, region)
mut.seq &lt;- codon_random(rgd.seq, keep = TRUE)
Biostrings::writeXStringSet(get_dna(mut.seq), "rgd.fasta")