In version 1.7 of UGENE there are 2 algorithms for DNA to reference assembly available.
And, yes, you're right, the first one is port of
Bowtie tool, which uses the Burrows-Wheeler based index. If you have a built index, you can use it as reference sequence. Read more about Bowtie
here.
The genome aligner tool is based on unique algorithm developed by UGENE team. There is a
documentation page available. It's not much, still you might find it helpful.
If you need more information on genome aligner tool or dna assembly usage, we'll be glad to answer your questions.