To analyze shotgun metagenomics data with the aim to get a taxonomic overview you could try the following software tools:

• Metaphlan (easy to install and use in my experience), first link/publication below
• MOCAT (offers more than just taxonomic abundance tables), second link/publication below

Hope you find these resources helpful!

http://huttenhower.sph.harvard.edu/metaphlan

http://vm-lux.embl.de/~kultima/MOCAT/

Article Metagenomic microbial community profiling using unique clade...

Article MOCAT: A Metagenomics Assembly and Gene Prediction Toolkit

Hi, do you have rRNA amplicon data or total DNA metagenomic data ? For the first you can use Mothur http://www.mothur.org/wiki/Main_Page, it can deal with 16S and 18S rRNA data. For the second case, you can still use Mothur for sequence processing, and for data analysis MGRAST online http://metagenomics.anl.gov/ or MEGAN http://www-ab.informatik.uni-tuebingen.de/software/megan5 on your own computer.

Hope it helps !

Hi Marcel,

For the fungal metagenoimc analysis (Phylogenetic/taxonomic analysis), you can use internal transcribed spacer (ITS) for the amplification/sequencing in place of 16S rdna (for bacterial).

1. Analysis of reads can be done using RDP classifier but you have to use separate database for fungal 18S/ITS sequences for example FungiDB. 

2. Analysis of the reads can be done using MEGAN software. 

http://ab.inf.uni-tuebingen.de/software/megan5/

QIIME can be used for the OTU analysis. You can refer the mentioned link below http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3712477/pdf/nph0199-0288.pdf

You can also use CloVR-ITS see the paper mentioned below.

CloVR-ITS: Automated internal transcribed spacer amplicon sequence analysis pipeline for the characterization of fungal microbiota 

Regarding the shotgun metagenomic sequence analysis you can use MG-RAST pipeline. 

May this will help you. 

To analyze shotgun metagenomics data with the aim to get a taxonomic overview you could try the following software tools:

• Metaphlan (easy to install and use in my experience), first link/publication below
• MOCAT (offers more than just taxonomic abundance tables), second link/publication below

Hope you find these resources helpful!

http://huttenhower.sph.harvard.edu/metaphlan

http://vm-lux.embl.de/~kultima/MOCAT/

Article Metagenomic microbial community profiling using unique clade...

Article MOCAT: A Metagenomics Assembly and Gene Prediction Toolkit

Hi Marcel,

As Fabian already said, you could make use of the MG-Rast software for metagenomics datasets. It is really friendly in use and had a clear overview manual. To upload the data everything is also explained step by step. I found MG-Rast a good tool to start with.

If you have an amplicon dataset and it's not to large, you could also make use of SILVA-NGS. It doesn't exist that long, but gives you some images about the taxonomy where you could start with.

Hope this helps you!

Several of these softwares are available free on the net like MEGAN, MOTHUR etc. They all come with detailed descriptions as to the purpose they are to be used for. Check and see which is most suitable for you. Good luck.

For the fungal metagenoimc analysis (Phylogenetic/taxonomic analysis), you can use Bioedit, simple software, even you can use CLUSTALW.

I agree with a previous suggestion made of MG-RAST.

J. Craig Venter Institute software resources might be helpful to your work too,

examine these at the provided link

link here

http://www.jcvi.org/cms/research/software/

I used MG-RAST, its a great program, give it a try..

MG-RAST is effective program. Try..

For Microbial metagenomics, go for Glimmer, Metaphlan will be another good choice.

According to MG-RAST manual, it is designed for prokaryotic metagenomics analysis "The system supports the analysis of the prokaryotic content of samples, analysis of viruses and

eukaryotic sequences is not currently supported, due to software limitations".