The UGENE Genome Aligner is a fast short read aligner. It aligns DNA sequences of various lengths to the reference genome with configurable mismatch rate.

It is available from the Tools ‣ DNA assembly submenu of the main menu.

     <img src="/wiki/download/attachments/4227719/UGENE Genome Aligner.png"/>

Select the Align short reads item to align short reads to a DNA sequence or Build index item to build an index for a DNA sequence which can be used to optimize aligning short reads to the sequence.