**5. Conclusions**

Profiling microbial communities from massive sequencing data constitutes a breaking point in the understanding of population structure and dynamics, their ecological functions and the complex relationships established between noncultivable microorganisms. Through technological developments such as nextgeneration sequencing and the developing of hundreds of open-access platforms, we have been able to better understand the role of the microbial world in natural ecosystems. This chapter intends to bring the use of computational biology tools to professionals in biological sciences with different expertise, interested in the world of metagenomics analysis. We have started with the basics of microbial community profiling through shotgun sequencing data and its processing using MetaPhlAn software (the reader will notice that there are other tools perhaps more appropriate to their conditions, an interesting option is the FOCUS software that works through a Web server). MetaPhlAn has the advantage of being fully integrated with the GraPhlan phylogenetic reconstruction tools. We dedicate a complete section to the 16S gene-based communities profiling; we illustrate the EzBioCloud platform, a useful tool to obtain ecological and phylogenetic information of microbiomes. An alternative approach to process assembled data is the use of Barrnap software, which is very fast and efficient to extract ribosomal sequences in assembled data, which can be subsequently clustered and processed with phylogenetic construction tools such as SeaView. Finally, we present a list of software that can serve as a guide for the analysis of microbiomes from their taxonomic characterization to the study of phylogenetic relationships between taxa.
