I need to know the analysis method for the bands resulting from DGGE since every band is not highly trusted for showing one species--if every band is not sequenced. I wonder if there are any softwares to analyze this.
It is also better to sequence the bands for better confirmation of the species available. Even in most of the cases sequencing is done after DGGE for further confirmation. You can also go for HRM analysis using Q-PCR. But sequencing gives better confirmation
You might try cutting your bands out, eluting them and then doing a restriction digest, but it would be terribly laborious, and you might have to reamplify your bands, with all the contamination problems that entails.
As far as analysing the gels goes, no software can beat the human eye, though some gel documentation software can help visual analysis.
There is software such as Gel Compar and Bionumerics produced by Applied Maths that can be used to help analysis your DGGE gels. However this software does require a license which is expensive so you would need to make sure that you will use the software a bit to make it worth the investment.
I'm also working with DGGE for community analysis. If you want to continue for sequencing, You need to repeat band excision, PCR for elutd DNA and run DGGE until you got one band from one poduct. it is the best way to get purify DNA for sequencig without cloning.