Question: Multiple sequence alignment and phylogenetic analysis
gravatar for l.roca
5.2 years ago by
l.roca10 wrote:



I have a theoretical question that puzzles me:

When I am doing an MSA (Multiple Sequence Alignment) some of the algorithm builds a guide tree. Therefore, why and what is the reason to build other trees when I do phylogenetic analysis?



alignment • 2.0k views
ADD COMMENTlink modified 5.2 years ago by Asaf6.8k • written 5.2 years ago by l.roca10

Different algorithms will give you different trees.  So if you generate a lot of them, you are more likely to get one that supports your conclusion!

ADD REPLYlink written 5.2 years ago by Brian Bushnell17k
gravatar for Asaf
5.2 years ago by
Asaf6.8k wrote:

If I understood your question correctly, you're asking why should you build a tree if the MSA algorithm gives you one.

There are many data you can use to build a tree, you can use DNA sequence, protein sequence, insertion sites etc. When you compare the sequences of one protein you get a tree based on this sequence, which can be true but can be biased from several reasons (different rate of evolution for instance). The tree will be valid but might be wrong. If you want to build a phylogenetic tree, you should consider the data you use and the algorithm you use to build the best tree you can.

ADD COMMENTlink written 5.2 years ago by Asaf6.8k
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