I hope this question may not come across as unintelligent. I was just wondering how does one, from a multiple sequence alignment, differentiate mutational hotspots or recombination from a region with polymorphisms, besides GC%?
My guess is that in a mutational hotspot the region of mutational events would be distributed across different sequences of the alignment, whereas a recombinational event would usually only apply to say one or two sequences of the entire alignment.
Would anyone like to add or elaborate on this concept?
Thank you very much
Edited by Pseudopneumo, 30 June 2012 - 03:03 PM.