I have used clonalframeML to find areas of recombination within my isolates, but I am unsure of how to remove these areas of recombination from each of my isolates sequence fasta. Can anyone help?
I can use cutSeq to extract the nucleotide sequences of recombination and am able to save these in separate fasta files. For example the output of cutSeq provides me with;
However how do I remove these sequences from the original fasta sequence? CutSeq only copies and pastes the recombination, but does not remove it.