As others have pointed out, two genes are homologs if they evolved from a common ancestor. Two genes are orthologs of each other if, in the gene family tree, the last common ancestor of those two genes was a speciation event. Two genes are paralogs of each other if, in the gene family tree, the last common ancestor of those two genes was a duplication event. This is important to know because after duplication, the genes are more likely to separately evolve more specific functions (subfunctionalization) or even new functions (neofunctionalization). Berkeley PHOG provides a precomputed database of orthologs derived from PhyloFacts gene family trees using tree distances. The default, most stringent variant, PHOG-S, aims to predict only clusters of genes which are all superorthologs of each other, that is, there are no duplication events in the portion of the gene family tree containing them. This variant has high precision but relatively lower sensitivity. The thresholded variant,... - Ruchira S. Datta

Good to see your thoughts on orthology at BioStar. - Khader Shameer

@kshameer Thanks! Your post inspired me to answer my first BioStar question. - Ruchira S. Datta