**1. Introduction**

Higher multicellular organisms have coexisted and co-evolved with resident microorganisms in a relatively harmonious relationship over millions of years, forming a complex organism called holobiont. These processes of co-evolution have been documented by several studies carried out in the organization and composition of host microorganisms (microbiome) in different species [1–4]. The microbiome is currently considered a functional organ which is fundamental for the host organism, given that studies have shown that this organ is highly dynamic and adaptable, likewise plays an important role in physiological adaptation processes,

metabolism, and development [1, 2, 4–6]. The study of the role of the microbiome for years was limited to those organisms that could be susceptible to culture, the use of techniques based on molecular information (AFLP and RFLP) and denaturing gradient gel electrophoresis (DGGE) could reveal the presence of some species not cultured, but the gel resolution was being the main limitation since a single band could contain more than one sequence [7]. The development of genomic tools such as the new generation sequencing platforms (NGS) has allowed a better resolution of the diversity present in a given sample through what is known as metagenomics [2, 7–10]. These same sequencing platforms have allowed not only observing the diversity of a host or environment, but also the functional role of microorganisms as well as their possible interactions with physiological processes or biogeochemical cycles through metatranscriptomics [1, 2, 4, 9]. The understanding of the composition of microorganisms, functions, interactions, and other biological processes through NGS has been done through the development of different bioinformatics tools, which make use of large amounts of information and are able to compare them through different data bases [3, 9, 11]. The objective of this chapter is to provide information on the different existing bioinformatics tools that have been used in studies of co-evolution and symbiosis in different models.
