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?
What's your reference? Or you use multiple alignment? I don't think you can use multiple alignement to align 200 genomes, so you must have a reference. You can just align the new genome to the reference.
I do have few complete genomes which can be used as reference. But what I want is to align multiple genomes to see gene loss, or gain and rearrangements. I know progressiveMauve can do this and also Mugsy can align multiple genomes. But what Im thinking of is if there is a way or tool to create a profile of multiple genome alignment and than use that profile to align any incoming new genome to all previously aligned genomes.
Yes, I think you are talking about multiple alignment. I don't think there exist any tools can do multiple alignment to 200 genomes (you may try and welcome to prove me wrong) for computation cost reason.
I agree with you that it would be computational very expensive to multiple align 200 genomes. I haven't tried doing it my self so I can't say if any tool can do it or not. But that's the reason I'm looking for an alternative approach which can be a profile based alignment where instead of aligning all 200 genome sequences with each other one can align each genome to a profile of previously created alignment with less number of genomes and thereby iteratively add new genomes to the alignment which I guess would be less computationally expensive as compare to previous approach.
I don't know any existing software can do that. If you find one, could you please post it here? Or if you can develop one, I believe it can be very promising (Can be a replacement of multiple alignemnt).