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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.

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    $\begingroup$ Welcome to BiologySE... thanks for your question. Do you think this is more of a programming question? If so, you may want to ask it on another SE site. Also, check out the help page for tips on how to ask a good question - you may want to edit and/or revise what you have to improve it. See this link: biology.stackexchange.com/help/how-to-ask $\endgroup$ – Vance L Albaugh Jul 4 '16 at 12:49
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You could decide to just insert the new clade next to some "closest" one ("closest" being defined in a clever way that remains to be devised), but it is possible that the result will be different from what you would obtain by reconstructing the phylogeny from scratch. The reason is that the information that the character combination in the new clade brings may alter the relationships between the other groups present in the data in a newly optimized phylogeny.

An example of application is that one typically wants to add more taxa in a phylogeny in oder to prevent long branch attraction.

As an aside remark: When one speaks of a "clade", one usually thinks of a bunch of terminal taxa (leafs of the tree): do you want to insert an whole bunch of taxa forming a monophyletic group, whose internal topology is already known, or just one terminal taxon?

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