AAI Matrix

Question

[matthewcrossie]

Hi all,

I've got a genome that potentially belongs in a novel family, and I want to do an All vs All AAI comparison of about 400 other genomes in the same order to create a matrix.

I've used CompareM to generate all possible combinations of AAI with each genome, but converting the output into a matrix is tricky and forms a table with a lot of blank values.

Are there any alternative programs that would be good for this sort of thing?

Thanks