We have a software package, BioNumerics, designed specifically for this purpose for prokaryotic genomes. It can handle starting from the reads as well as from the assembled sequences. You can do SNP detection on mapped genomes, but also align de novo sequences and perform a mutation analysis on the aligned sequences. You can ask for a free trial to test it yourself.
You would probably get more useful answers if you explained in more detail your data. I'll give two suggestions, under two different assumptions:
1) You have assembled genomes and no sequencing data: use Mauve, it aligns full and draft genomes and has a function to export SNPs.
2) You have Illumina sequencing data: use A5_MiSeq, it produces really goods assemblies, is easy to install and use. You could then use the BAM file it outputs to perform variant calling with SAMtools, there are lots of good tutorials around the web.