Index _ | A | B | C | D | F | G | I | K | M | N | P | R | S | T _ __getitem__() (pyfamsa.Alignment method) __init__() (pyfamsa.Aligner method) (pyfamsa.Alignment method) (pyfamsa.GappedSequence method) (pyfamsa.Sequence method) __len__() (pyfamsa.Alignment method) A align() (pyfamsa.Aligner method) align_profiles() (pyfamsa.Aligner method) Aligner (class in pyfamsa) Alignment (class in pyfamsa) B build_tree() (pyfamsa.Aligner method) C cluster_fraction (pyfamsa.Aligner attribute) cluster_iters (pyfamsa.Aligner attribute) copy() (pyfamsa.Alignment method) (pyfamsa.GappedSequence method) (pyfamsa.Sequence method) D dump() (pyfamsa.GuideTree method) dumps() (pyfamsa.GuideTree method) F FAMSA_ALPHABET (in module pyfamsa) famsa_info() (in module pyfamsa) G gapped_size (pyfamsa.GappedSequence attribute) GappedSequence (class in pyfamsa) guide_tree (pyfamsa.Aligner attribute) GuideTree (class in pyfamsa) I id (pyfamsa.GappedSequence attribute) (pyfamsa.Sequence attribute) K keep_duplicates (pyfamsa.Aligner attribute) M medoid_evaluations (pyfamsa.Aligner attribute) medoid_sample (pyfamsa.Aligner attribute) medoid_seeds (pyfamsa.Aligner attribute) medoid_threshold (pyfamsa.Aligner attribute) MIQS (in module pyfamsa) N n_refinements (pyfamsa.Aligner attribute) names (pyfamsa.GuideTree attribute) P PFASUM31 (in module pyfamsa) PFASUM43 (in module pyfamsa) PFASUM60 (in module pyfamsa) R refine (pyfamsa.Aligner attribute) S scoring_matrix (pyfamsa.Aligner attribute) Sequence (class in pyfamsa) sequence (pyfamsa.GappedSequence attribute) (pyfamsa.Sequence attribute) size (pyfamsa.GappedSequence attribute) (pyfamsa.Sequence attribute) T threads (pyfamsa.Aligner attribute) tree_heuristic (pyfamsa.Aligner attribute)