**Abstract**

Phylogenetic relationships among microbial taxa in natural environments provide key insights into the mechanisms that shape community structure and functions. In this chapter, we address the current methodologies to carry out community structure profiling, using single-copy markers and the small subunit of the rRNA gene to measure phylogenetic diversity from next-generation sequencing data. Furthermore, the huge amount of data from metagenomics studies across the world has allowed us to assemble thousands of draft genomes, making necessary the comparison of whole genomes composites through phylogenomic approximations. Several computational tools are available to carry out these analyses with considerable success; we present a compendium of those open source tools, easy to use and with modest hardware requirements, with the aim that they can be applied by biologists non-specialists to study microbial diversity in a phylogenetic context.

**Keywords:** metagenomics profiling, phylogenetic diversity, phylogenetic metadata representation
