Homology::subtype() is deprecated

(cherry picked from commit f3f0244664c2d66a6e9c39263a235c1290ac7e80)
new "is_tree_compliant" option in fetch_all_by_MethodLinkSpeciesSet()
new option to select a subset of species_tree_nodes
Filtering in/out-parologues is done server-side
Documentation
_filter_paralogues_by_ancestral_species() can be removed