I have two incomplete whole genome sequencing data belong to Helicobacter pylori strains. They are done by using Illumina Hiseq 2000 platform. Both of the strains are MLST identical, meaning there are derived from the same strains, only that they are phenotypically different. I would like to know the if there is any mutation occurs throughout the experiment, may I know if they is any way to do the whole genome alignment on them? I tried using cluster W and Muscle on MEGA5, apparently the data is too large for it. May I know if there is any other software that allow whole genome alignment? Besides, should I concatenate the contigs together in order prior for the alignment? Your advice is highly appreciated.