The phage proteomic tree is a unifying proteomic taxonomy for viruses. The problem with viruses is that there is no single gene that can be used for taxonomy, and so you have to combine distances some how.
In 1999, Edwards and Rohwer started testing different techniques for combining taxonomy of viruses, and comparing them to known literature. We had less than 50 phage genomes in the first iterations, but by the time of publication in 2002 there were 105 complete phage genomes. Now there are thousands.
This code is the original code (some of it has been slightly updated to fix major bugs) to generate the phage proteomic tree.
In the directory spounavirus we walk through building a phage proteomic tree for 93 spounaviridae as part of a joint collaborative effort that Evelien Adriaenssens is organising.