Removing recombination from sequence alignment

Question

[natasha]

Hi

I have detected regions of recombination in a multi sequence alignment of 50 bacterial isolates using Clonal Frame ML. How do I remove these regions from the multi fasta?

I do not want to mask these regions, just remove them entirely.

Thanks for your help!

[Bioinformatics_NewComer]

BRAT and Gubbins might help.

It really "depends" how you want to work, and at what stage of your data.

[natasha]

I've also used Gubbins, but I get the same problem - it detects the areas of recombination in my multi sequence alignment but does not remove them. How do I remove these regions from my origional fasta?

[Bioinformatics_NewComer]

Hi,

Sorry, don't know of that. I proceed by removing Recombinant region from MSA.

[natasha]

Hi, sorry my mistake - I meant to say, how do I remove the regions of recombination from MSA?

[Bioinformatics_NewComer]

From my understanding of gubbins, the final output you get is post removal of re-combinant region. Your input is an MSA. Your output is de-noised MSA.