It seems to me that if you believe that these sequences are identical at many
positions because they derive from a common ancestor then you can feel
justified in using "homology" and do this knowing that you are implying an
inference. You may in this case wish to distinguish paralogous from
orthologous. (see Patterson's introduction to Molecules and Morphology in
Evolution: Conflict or Compromise)
Briefly these terms distinguish between identities that exists because
of shared ancestor of 2 species (orthologous) and identities that come from a
gene duplication event within a linneage (think of all of the proteins that have
Ig like domains). You seem to feel that you have orthologous sequences that
share many identities.
As an aside, molecular biologists seem much more willing to use
homology to mean "it looks the same (= same sequences)" and morphologists
prefer to insist that homology indicates a stronger statement of the reason for
the similarity (homology -> derived from a common ancestor).
Jeremy Ahouse
Brandeis University - Biophysics
