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This document summarizes steps in a bioinformatics analysis pipeline involving BLAST, ClustalW, and SOAP. It describes running BLAST to identify sequences producing significant alignments to a query sequence and extracting identifier, name, and e-value information from BLAST results. It then discusses using ClustalW for multiple sequence alignment and SOAP for visualization of alignment and phylogenetic tree results. The document provides code snippets and filenames involved in steps for the analysis pipeline.