Get representative sequence without distance matrix?

I was wondering if it is possible to get a representative sequence for all phylotypes without having a .dist file? I’ve been forced to use the phylotype method for my illumina sequencing because our paired reads don’t fully overlap, creating a ridiculously large distance matrix. I would really like to get a representative sequence for each phylotype, but it appears like I am required to have a distance file. Can you suggest any way around this requirement? I really appreciate your help!

The get.oturep command has two methods for finding a representative: distance and abundance. The distance method is the default and requires and distance matrix, but the abundance method just requires a name or count file.