Can anybody help me to do the community structure analysis using 16S RNA gene probes. Is there any reliable method other than NSG? Is there any software to analysis the community structure/ abundance?
Although it is bit old but you can use DGGE and analysis the band pattern by Gelcompare II software. Interest of ribotype can be sequenced.
I think you should be able to use Mothour, Qiime and clovr as well. Personally I liked the gel compare program. It is one of the easier ones to learn.
Community structure and abundances can be analyzed using the Vegan package in R.
http://vegan.r-forge.r-project.org/
You might also want to check this method for 16S rRNA community analysis:
Multivariate Analysis of Complex DNA Sequence Electropherograms for High-Throughput Quantitative Analysis of Mixed Microbial Populations
http://aem.asm.org/content/73/15/4975.full
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