AMPHORA ("AutoMated Phylogenomic infeRence Application") is an open-source bioinformatics workflow. AMPHORA2 uses 31 bacterial and 104 archaeal phylogenetic marker genes for inferring phylogenetic information from metagenomic datasets. Most of the marker genes are single copy genes, therefore AMPHORA2 is suitable for inferring the accurate taxonomic composition of bacterial and archaeal communities from metagenomic shotgun sequencing data.

An amphora (English plural: amphorae or amphoras) is a type of container of a characteristic shape and size, descending from at least as early as the Neolithic Period. Amphorae were used in vast numbers for the transport and storage of various products, both liquid and dry, but mostly for wine. It is most often ceramic, but examples in metals and other materials have been found.