if msa != nil
seq = get_sequence( query, msa )
species = get_species( seq )
raise StandardError, "could not get species" if species == nil || species.empty?
if x_models != nil && x_models.length > 0
if msa != nil
seq = get_sequence( query, msa )
species = get_species( seq )
raise StandardError, "could not get species" if species == nil || species.empty?
if x_models != nil && x_models.length > 0