Developed to address the need to identify orthologs. InParanoid uses the pairwise similarity scores, calculated using NCBI-Blast, between two complete proteomes for constructing orthology groups. An orthology group is initially composed of two so-called seed orthologs that are found by two-way best hits between two proteomes. More sequences are added to the group if there are sequences in the two proteomes that are closer to the corresponding seed ortholog than to any sequence in the other proteome. These members of an orthology group are called inparalogs. A confidence value is provided for each inparalog that shows how closely related it is to its seed ortholog.