I want to compare two genomes that I obtained from my shotgun metagenomic sequencing data. Seems like "cd-hit-est-2d" option works perfectly for me as I need to find out what sequences are similar/dissimilar between these two genomes. However, I read in the CD-HIT manual that it's good for non-intron containing sequences e.g. EST. That means I SHOULD NOT use CD-HIT for my metagenome comparison?
If not, please suggest any other tool that I can use to compare the genomes.
Many thanks in advance!