How to intrepret Polygenic tree

[hi.singh]

I have generated a polygenic tree (Clustal W) using different virus strains and using Fasta format. But how do I find out which is the best strain I should recomend for the vaccine? Is it the topmost branch in tree?
I have the tree in file but I do not know how to upload it here?[/img]

[jenniferpaulson]

Hi Harsh,

It seems like you're on the right track and have gotten through many obstacles already, since you have already generated a polygenic tree. Now you just need to interpret your result.

The simplest explaination is that Clustal W has determined how similar your sequences (strains) are to each other, and that similarity is reflected by how close they are to one another in the tree. So a short distance from one branch of the tree to another means that those strains are very similar, and a long distance from one branch to another means that those strains are not very similar.

Try looking for a help or FAQ link from the page where you used ClustalW for a more detailed explaination.

Without knowing more about your project, I can't say which strain that you should use for your vaccine. Does knowing which strains are very similar to each other help you decide?

Good luck with your project.

Jennifer