I have found out the core ortholog set (Core Genome) of 30 bacterial strains using NCBI Blast Package. But finding Pan Genome (Unique genes + accessory genes + Core genes) of same dataset of 30 organisms is becoming hectic. As it is not possible to align each genome with other, around overall 900 times. I can`t derive any other logical pattern so that I can determine the accessory genes without repeats. Please help. Thanks in advance.
You probably would not need to align every gene against every other (if that's what you meant above). A simpler technique would be to add keep adding genes to a database if they are sufficiently different from the genes that are already there. As you perform the alignments you will need a simple program to tabulate which genes have been hit just once over the entire process (these are the unique), genes that were hit for every strain (core genes) the rest are the accessories.
You might also want to consult what the literature says:
I was working on this since I asked this question and after this long work I, Myself built one tool which I named BPGA-Bacterial Pan Genome Analysis pipeline.
Along with core, accessory and unique genes, it also has many features like functional and pathway assignments and statistics and more.
It is available at my souceforge page