Hi, I've generated three binned genomes from soil metagenome samples. These binned genomes are collections of contigs, and I would like to find a program that could efficiently perform an alignment of all three of these binned genomes at once and find regions that are different between all three of them, in order to create diagnostic primers for qPCR. Thanks for any help!
Any multiple sequence alignment program can do the alignment, but no program can decide what can be used for the primer designing. Either do manual primer designing or use primer blast to get primers. In second step you will be evaluating primers on your bins and check if they are targeting different regions.
You can also give a try to Nucmer ( http://mummer.sourceforge.net/ ). But as was already said, you will have to inspect the alignments manually to find regions of interest for your qPCRs
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