Suppose we have an alignment. When a phylogeny tool (PhyML in this case) is used on this alignment, a tree consisting of 5 clades is returned.
The thing is: suppose we have this alignment on a web site, and some user uploads a new sequence to add to this alignment. After realign with the new sequence, phylogeny inference is applied, and then, a tree visualizer.
I'd like to know which one of the 5 clades contains the new sequence (if any), without the need of looking at the tree.
How should I approach this issue? I think that first of all, I should define my clades (how to?), and then, measure distances from my new sequence, to all clades, and keep the one with the shortest distance...But I'm not sure if this is a good strategy (not to say I'm not sure how to accomplish this..)
This is maybe more of a concept question...
I'm working with biopython.