Removing recombination from sequence alignment
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!
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BRAT and Gubbins might help.
It really "depends" how you want to work, and at what stage of your data.
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?
Hi,
Sorry, don't know of that. I proceed by removing Recombinant region from MSA.
Hi, sorry my mistake - I meant to say, how do I remove the regions of recombination from MSA?
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.