Bowtie
Bowtie is a popular short read aligner. Click this link to open the Bowtie homepage. Bowtie is integrated as an external tool into UGENE.
Open the Tools ‣ NGS data analysis item submenu of the main menu.
Select the Map reads to reference option to align short reads to a DNA sequence using Bowtie. Alternatively, select the Build index to reads mapping option to create an index for a DNA sequence, which can be used to improve the efficiency of aligning the short reads to the sequence.