  The human microbiome is the ensemble of genes in the microbes that live
inside and on the surface of humans. Because microbial sequencing information
is now much easier to come by than phenotypic information, there has been an
explosion of sequencing and genetic analysis of microbiome samples. Much of the
analytical work for these sequences involves phylogenetics, at least
indirectly, but methodology has developed in a somewhat different direction
than for other applications of phylogenetics. In this paper I review the field
and its methods from the perspective of a phylogeneticist, as well as
describing current challenges for phylogenetics coming from this type of work.
