Recombination detection tutorial

Question

[a.alsayed.phd]

Please, can anyone help in step-by-step tutorial on how to assess if there is any recombination events in virus if I have Sanger sequences, MSA., phylogenetic tree, etc? Many Thanks in advance

Answer 1

[babin.yurii]

Actually, I have not ever encountered any step-by-step guide. But you can try the following tools to search for recombination: T-Recs, RAT, RDP-4, Simplot, Swe-blast, etc. There is a whole bunch of them. Some of them are outdated, some of them throw unexpected exception. But still, this is the way somehow to start.