Do you have 16S data or whole metagenomes? These two data types are very different. If you have 16S data, QIIME and QIIME2 are frequently used and you have a lot of different options and algorithms to choose from. If you have metagenomes, kraken or kaiju might be interesting for read classification; or CAT (Univ. Utrecht) if you want to classify contigs.

Use MEGA 7.0 software tool for phylogenetic analysis. There are other tools like DECIPHER, Ribosomal Database Project, Naive Bayesian Classifier 2.5 and USEARCH. You can use them for various analysis. Please find the latest paper in attached link for further details:

Article Retrieved 16S rRNA and nifH sequences reveal co-dominance of...

You can get your metagenomic data analysed through the MG-RAST server. It is one of the most widely used servers for analysis of NGS data for microbiome analyses.

http://metagenomics.anl.gov/

Best of luck

SD

Good job

As Sibnarayan said, MG_RAST is a powerful server for metagenome analysis. Its friendly used and kept updated and under development.

MEGAN6 is available for free from the University of Tuebingen, and is supposed to be user-friendly and powerful: http://ab.inf.uni-tuebingen.de/software/megan6/.

@ Melissa Luanne Cox Thank you very much :)

Do you have 16S data or whole metagenomes? These two data types are very different. If you have 16S data, QIIME and QIIME2 are frequently used and you have a lot of different options and algorithms to choose from. If you have metagenomes, kraken or kaiju might be interesting for read classification; or CAT (Univ. Utrecht) if you want to classify contigs.

Many tools could be used, MG RAST is simple to use and very good tool because join database and tools, but is a litlle limited in analysis...

Another option similar to MG RAST, but less known is EBI metagenomics

https://www.ebi.ac.uk/metagenomics/

Megan is very good too, many researchs use this tool :

http://ab.inf.uni-tuebingen.de/software/megan6/

QIIME is good tool, has many tutorial http://qiime.org/

LIke QIIME, MIcca and BMP are good tools to work with 16S data.

http://www.brmicrobiome.org/

http://micca.org/

Kraken is very powerful option to analyse wgs, but it needs lots of memory RAM, another option is CLARK:

http://clark.cs.ucr.edu/

As suggested by members, MG-RAST is a good and user-friendly pipeline. QIIME is a little tricky but very powerful in terms of OTU and statistics calculations. You would need to perform some statistical analysis for your data like finding out diversity indices like Shannon index and creating PCO plots for comparative analysis. For this you would need some other tools.

This is one other tool i found which may be helpful http://www.microbiomeanalyst.ca/

@ Garima Ayachit Thank you very much