For a pair of homologous genes, finding out whether they are orthologs - stemming from a speciation - or paralogs - stemming from a gene duplication - is of central importance in computational biology. An orthologous relation enables, for instance, functional equivalence of the two genes to be inferred. A major approach to orthology analysis is to contrast the gene family evolution with the species evolution, most commonly using the most parsimonious reconciliation (MPR). However, most MPR methods first infer the gene tree without considering the species tree, then reconcile the trees.

The Method

We propose a sound, comprehensive method, DLRSOrthology, to infer gene trees in light of the species tree, while simultaneously computing probabilistic estimates of orthology for each extant gene pair. During inference, the model jointly takes into account the reconciliation and the strong signal conveyed by sequences.

The Tool

Based on the algorithm, we have an implementation for the DLRSOrthology. Please visit DLRSOrthology homepage for more info.