> orthology - where the two sequences encode the same protein,
> e.g. a myoglobin in a human and a myoglobin in a whale
>> paralogy - where the relationship between the two sequences
> is not consistent with the phylogeny, e.g. myoglobin in a human
> and beta-globin in a human (here, the ancestor of myoglobin
> and hemoglobin is much older than recent ancestors of humans).
I think that you might what to distinguish these terms not with respect to
phylogentic consistency but rather in terms of genetic events. A gene
duplication (that gives rise to a pair of paralogous genes) may happen before a
linneage split. If the 2 genes become functionally diiferent in the 2
linneages you may be fooled into imagining a homology that is due to a shared
derived gene when in fact you don't have orthologous genes because of the
paralogy in the ancestor.