Hello. I am looking for a tool or a methodology to make whole genome alignments with 50+ genomes. I used to use Gegenees that basically construct a matrix (heatmap) of similarity based on all vs all BLAST results. Recently, Gegenees stopped working and I don't know the reason. It might be because I've updated my Java version. It prints out some errors related to eclipse (which I don't know what it is). Anyways, is there any other tool or method similar to Gegenees? I need to know the similarity percentage between the organisms I am working with in order to define cut-off values for pan-genome analysis. Thank you!