The relationships between retroviral proteases. Protease sequences from several different immunodeficiency viruses are compared with endogenous retroviral sequences found in various eukaryotic genomes. The numbers in brackets indicate GenBank accession numbers ; viral strains are indicated by subscript letters. Nucleic-acid sequences were aligned using ClustalW  and a Jukes-Cantor phylogenetic tree file was generated using the PHYLIP package and the programs DNADIST and FITCH. The tree was produced using the cladogram option and the programs TreeView. Abbreviations: BIV, bovine immunodeficiency virus; EIAV, equine infectious anemia virus; FIV, feline immunodeficiency virus; HERV, human endogenous retrovirus; SIV, simian immunodeficiency virus.