What is the difference between a guide tree and ...
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What is the difference between a guide tree and a true phylogenetic tree?
A guide tree is calculated based on the distance matrix that is generated from the pairwise scores. The output can be found in the .dnd file. A phylogenetic tree is calculated based on the multiple alignment that it receives. The distances between the sequences in the alignment are calculated and can be found in the .ph file. These distances are then used by the method chosen (nj, phylip, dist) to make the phylogenetic tree (.nj, .ph, .dst file).
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