I am looking for whole genome aligning software to align around 150 bacterial genomes (within same species). I am trying to find phage hotspots on genome so I would want to keep the coordinates on the same level. This means the length of alignment can be many Mb longer just in order to keep the same (synteny?) blocks in the same "column". Something like Ragout, which maps unassembled contigs on reference genome and adds N's where there is gaps, but in multi alignment scale. I tried Mauve, but it doesn't serve the purpose.
Sorry for unclear question, I'm just learning the basics of bioinformatics. Thank you.