Retaining recombinant free non-polymorphic sites

[ramadatta]

Is there a way in gubbins to generate a fasta file which can retain recombinantion free regions of both non-polymorphic sites and polymorphic sites from the alignment ? At present gubbins seems to only generate recombinantion free regions of polymorphic sites in fasta file. Thanks

[andrewjpage]

This is not currently one of the supported outputs. You could have to use the *.recombination_predictions.gff file to mask out your original alignment.

[MostafaYA]

@ramadatta
As a note, I am not sure if this tool can help you (https://github.com/kwongj/maskrc-svg). It basically masks the recombinant regions in the initial alignment file that used for Gubbins.

[ramadatta]

@MostafaYA Thanks much! I am using this now with success.