Using an alternative aligner with MapSplice

[beans]

Hello there,

I'm starting out using RNA-seq data to identify/ quantify alternative splicing in a variety of species. I'd like to use MapSplice as it seems quite flexible and performs well but I'd like to use an alternative alignment tool to Bowtie, like SHRiMP. I've read through the user guide and I can't see how to do this - does anyone out there know? I hope it's an simple oversight on my behalf!

Thanks in advance