Genome comparisons

We would like to edit the Perl tool that currently compares start and stop codons from the same species in three different annotations, or find an existing tool that will do the following: We would like this tool to compare our Halomicrobium mukohataei genome to 9 other halophile’s genomes all using the annotations from RAST. Basically, the Perl script should take all the known H. mukohataei amino acid sequences from RAST and compare these (in a Blastp manner) to all 9 other halophile genomes. In this manner, we will be able to determine which genes in H. mukohataei are conserved among other halophiles and which are unique to this species. The other 9 species we would like to compare are:
Haloarcula sp 33799
Haloarcula sp 33800
Haloarcula vallismortis
Haloferax denitrificans
Haloferax mediterranei
Haloferax mucosum
Haloferax sulfurifontis
Haloferax volcanii
Halorhabdus utahensis