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#[] Bio::BioAlignment::CodonSequence
#[] Bio::BioAlignment::Sequence
#codon_table Bio::BioAlignment::Codon
#each Bio::BioAlignment::Sequence
#each Bio::BioAlignment::Alignment
#each Bio::BioAlignment::CodonSequence
#gap? Bio::BioAlignment::Element
#gap? Bio::BioAlignment::Codon
#id Bio::BioAlignment::Sequence
#id Bio::BioAlignment::CodonSequence
#initialize Bio::BioAlignment::Sequence
#initialize Bio::BioAlignment::Codon
#initialize Bio::BioAlignment::Alignment
#initialize Bio::BioAlignment::CodonSequence
#initialize Bio::BioAlignment::Element
#pal2nal Bio::BioAlignment::Pal2Nal
#seq Bio::BioAlignment::CodonSequence
#seq Bio::BioAlignment::Sequence
#sequences Bio::BioAlignment::Alignment
#to_aa Bio::BioAlignment::CodonSequence
#to_aa Bio::BioAlignment::Codon
#to_nt Bio::BioAlignment::CodonSequence
#to_s Bio::BioAlignment::Codon
#to_s Bio::BioAlignment::CodonSequence
#to_s Bio::BioAlignment::Sequence
#to_s Bio::BioAlignment::Element
#undefined? Bio::BioAlignment::Codon