For that many bacterial genomes, whole genome alignment would either be impractical or might take very long time and require lots of computational resources to properly align them especially if working with a species that has high rates of genetic recombination/horizontal gene transfer such as Streptococcus pneumoniae. In such species, most people usually work with a core genome alignment (merged alignment of all the genes present in a species/dataset) for phylogenetic analysis etc. This approach would not be appropriate if you're particularly interested in non-coding regions for example, rearrangements etc.

Tools that you could use are; GET_HOMOLOGUES (http://www.ncbi.nlm.nih.gov/pubmed/24096415), ROARY (https://github.com/sanger-pathogens/Roary), CD-HIT (http://weizhong-lab.ucsd.edu/cd-hit/download.php).

Please have a look: http://mugsy.sourceforge.net/

http://genome.cshlp.org/content/14/7/1394.short