Scripts to analyse recombination sites identified in bacteria
Removes the sites of recombination identified by ClonalFrameML from an alignment file. The program removes sites mentioned in the importation_status file from ClonalFrameML.
python3 CFML_sitesremover.py -f <Recomb sites> -i <Input fasta> -o <Output fasta>
-f Recombination sites specified in importation_status.txt of ClonalFrameML
-i Input fasta filename
-o Output fasta filename