From release 3.0, MetaPhOrs is the method used by PhylomeDB for providing orthology predictions.

MetaPhOrs is a meta-method to predict orthology and paralogy from multiple phylogenetic evidence. To maximize reliability and coverage, we retrieved gene trees from PhylomeDB, Ensembl, TreeFam, and Orthogroups. In addition we built maximum likelihood trees for orthologous gene families in OrthoMCL, COG, and EggNOG. The resulting ~700.000 gene family trees provide information on orthology and paralogy relationships for over 300 million protein pairs over 829 fully-sequenced genomes. Taking advantage of the (partial) overlap between trees from different sources we compute a consistency score which, together with the number of independent sources used, is a good proxy for the reliability of the predictions.

Thus, although the orthology table will indicate whether a given orthology (or paralogy) prediction is supported by the tree you are looking at, the actual predictions will be informed in all other trees from that contain that pair of homologs. A consistency score will indicate the fraction of evaluated trees that support that prediction and the evidence level, will tell you how many independent sources were used. Both measures can be used as a proxy for the actual reliability of the prediction.

You can retreive use the MetaPhOrs webserver to retrieve orthologs and paralogs from a given pair of genomes, or a list of protein IDs, etc.

You can have more information on the method at the following publication:

Pryszcz LP, Huerta-Cepas J and Gabaldón T. (2010) MetaPhOrs: orthology and paralogy predictions from multiple phylogenetic evidence using a consistency-based confidence score. Nucleic Acids Research.