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.
4.9 years ago by
Asaf ♦ 6.3k