Allows genome tree reconstruction and metagenomic phylotyping. AMPHORA is an application for large-scale protein phylogenetic analysis. The software supports the analyses of DNA sequences, which means that users can apply AMPHORA2 directly to metagenomic reads without the need to first annotate the sequence. It can phylotype metagenomic sequences from a mixed population of bacteria and archaea and should be useful for the study of microbial evolution and ecology in the genomic era. A web application and a flavor of AMPHOR2 are also available.