Actually what i want to know is that do we have access to the codes of the software.
You can use QIIME. Its free and all the codes are publicly available.
You can use QIIME. Its free and all the codes are publicly available.
There are two frequently used free software packages available. One is QIIME (http://qiime.org/) as pointed out by Emine and another one is mothur (https://www.mothur.org/). While I prefer mothur they both have their advantages and disadvantages as described in this nice blogpost http://blog.mothur.org/2016/01/12/mothur-and-qiime/
You can use QIIme, always complemented with other tools (cutadapt, UCHIME, Acacia etc). CLC workbench has also aMicrobial Genomics Module. However is not free and at the end is a black box where you don't know, what exactly the program did. However, If you want the command line codes, I strongly recommend this:
https://www.ncbi.nlm.nih.gov/pubmed/?term=Assessing+Bacterial+and+Fungal+Diversity+in+the+Plant+Endosphere
This paper has all the codes and might be what you need.
Thank you all, for your kind answers. The information was very helpful.
with my kind regards and appreciates,
koray
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