Why do the BLAST search results differ between Simple Homology Modeling (and Residue Scanning) and the Advanced Homology Modeling?

This difference is due to the fact that in Simple Homology Modeling and Residue Scanning, the sequences are realigned using ClustalW and are also ordered based on sequence identity. In Advanced Homology Modeling, the realignment and reordering is not done, but rather the templates are used directly in the order in which they are returned from BLAST.

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