To start working with APR file you can open it in the Alignment Editor in read-only mode or convert it to another format.
To do this, open the *.apr file. The following dialog will appear:
If you choose the first option the file will be opened in the Alignment Editor as multiple sequence alignment in read-only mode. If you choose the second option the file will be converted to a corresponding format and open in UGENE.
The following formats are available: CLUSTALW, FASTA, Mega, MSF, NEXUS, Phylip Interleaved, Phylip Sequential, Stockholm