When you select the Tools ‣ Align to reference ‣ Align short reads item in the main menu, the Align Sequencing Reads dialog appears. Set value of the Align short reads method parameter to BWA-SW. The dialog looks as follows:

<center>
     <br>
     <img src="/wiki/download/attachments/6062167/Aligning Short Reads with BWA-SW.png"/>
     <br>
</center>

There are the following parameters:

Reference sequence — DNA sequence to align short reads to. This parameter is required.

Result file name — file in SAM format to write the result of the alignment into. This parameter is required.

Prebuilt index — check this box to use an index file instead of a source reference sequence. Also you can build it manually.

SAM output — always save the output file in the SAM format (the option is disabled for BWA).

Short reads — each added short read is a small DNA sequence file. At least one read should be added.

You can also configure other parameters. 

Score for a match — maximum edit distance. An integer value should be input.

Mismatch penalty — the fraction of missing alignments given 2% uniform base error rate. A float value is used.

Gap open penalty — maximum number of gap opens.

Gap extention penalty — algorithm for constructing BWT index.

Band width - 

Mask level - 

Number of threads - 

Size of chunk of reads - 

Score threshold (divided by much score) - 

Z-best - 

Number of seeds to start rev alignment - 

Prefer hard clipping in SAM output - 

Select the required parameters and press the Start button.