I'm trying to do whole genome alignment for more than 200 bacterial genomes (both finished and draft). I know there are nice tools to do this alignment such as Mugsy, Mauve, Mumer etc. But now my question is after once I finish aligning this 200 genomes using any of these tools, is there a method or tool that will allow me to iteratively align new genome to existing alignment without realigning all the previously aligned genomes. I guess some thing similar to HMM based profile alignment would be required to do it. But I'm not sure if there is any method already developed to do it. Can anyone suggest me about method or way to do this type of alignment?