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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Other Frequently Asked Questions

• Is it possible to perform bootstrap analysis or to get the Bootstrap values along with the nodes of each branch of the phylogram?
• What are the default parameters used by ClustalW?
• How do I reference use of this service?
• How can I see the parameter values that are used by the ClustalW program?
• Why does Jalview not work for me?
• How does Clustalw Work (very simple explanation)?
• What type of sequences can ClustalW align?
• How are the pairwise alignment scores generated?
• What is the difference between a cladogram and a phylogram?
• Why use ClustalW?
• More...