Hello again!
Now that I have my basic trees sorted out, I would like to look at my collection of viral genome sequences on a gene-by-gene basis to see if any sites are under positive selection.
The genome variation between taxons is pretty low (~1.5% over 5Kb), so from my very basic understanding, I should use the REL method, which works well for low-diversity alignments, right?
I input my alignment into the REL app on the Datamonkey.org site, and got some results that I was puzzled by. My most vairable gene showed that I only had sites under negative selection, and the output was sensitive to the number or sequences thatI would put in, despite identical sequences being pruned out prior to analyses apparently.
Am I missing something fundemental here?
0
No replies to this topic
