Bowtie 2 is a popular ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences. Click this link to open Bowtie 2 homepage. Bowtie 2 is embedded as an external tool into UGENE.

Open Tools ‣ Align to reference submenu of the main menu.

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Select the Align short reads item to align short reads to a DNA sequence. 

Or select the Build index item to build an index for a DNA sequence which can be used to optimize aligning of the short reads to the sequence: