Here it depends on what you are looking for. If you want a single, semi global alignment (with at most non-overlapping alternatives) then bwa-mem will do the job.

If you want to look at all possible alignments then you will need to use a generic aligner such as lastz or last

• http://www.bx.psu.edu/~rsharris/lastz/
• http://last.cbrc.jp/

consolidating the information out of all the alternatives these tools may produce may be more challenging.