PhenIX, Phenotypic Interpretation of eXomes, is a pipeline for ranking (prioritizing) candidate genes in exomes or NGS panels with comprehensive coverage of human Mendelian disease genes. It ranks genes based on predicted variant pathogenicity as well as phenotypic similarity of diseases associated with the genes harboring these variants to the phenotypic profile of the individual being investigated, based on analysis powered by the Human Phenotype Ontology (HPO).

The method has been published in Science Translational Medicine:

Effective diagnosis of genetic disease by computational phenotype analysis of the disease-associated genome
Zemojtel T*, Köhler S*, Mackenroth L*, Jäger M, Hecht J, Krawitz P, Graul-Neumann L, Doelken S, Ehmke N, Spielmann M, Oien NC, Schweiger MR, Krüger U, Frommer G, Fischer B, Kornak U, Flöttmann R, Ardeshirdavani A, Moreau Y, Lewis SE, Haendel M, Smedley D, Horn D, Mundlos S, Robinson PN.
Sci Transl Med. 2014 Sep 3;6(252):252ra123. doi: 10.1126/scitranslmed.3009262.

The tool is available on this website.