Index _ | A | B | C | D | F | L | M | N | O | P | R | S | T _ __getitem__() (pytrimal.AlignmentResidues method) (pytrimal.AlignmentSequences method) __init__() (pytrimal.Alignment method) (pytrimal.AutomaticTrimmer method) (pytrimal.BaseTrimmer method) (pytrimal.ManualTrimmer method) (pytrimal.OverlapTrimmer method) (pytrimal.RepresentativeTrimmer method) (pytrimal.SimilarityMatrix method) (pytrimal.TrimmedAlignment method) __len__() (pytrimal.AlignmentResidues method) (pytrimal.AlignmentSequences method) A aa() (pytrimal.SimilarityMatrix method) Alignment (class in pytrimal) AlignmentResidues (class in pytrimal) AlignmentSequences (class in pytrimal) AutomaticTrimmer (class in pytrimal) B BaseTrimmer (class in pytrimal) C copy() (pytrimal.Alignment method) (pytrimal.TrimmedAlignment method) D distance() (pytrimal.SimilarityMatrix method) dump() (pytrimal.Alignment method) dumps() (pytrimal.Alignment method) F from_biopython() (pytrimal.Alignment method) from_pyhmmer() (pytrimal.Alignment method) L load() (pytrimal.Alignment method) (pytrimal.TrimmedAlignment method) M ManualTrimmer (class in pytrimal) N names (pytrimal.Alignment attribute) nt() (pytrimal.SimilarityMatrix method) O original_alignment() (pytrimal.TrimmedAlignment method) OverlapTrimmer (class in pytrimal) P platform (pytrimal.AutomaticTrimmer attribute) (pytrimal.BaseTrimmer attribute) (pytrimal.ManualTrimmer attribute) (pytrimal.OverlapTrimmer attribute) (pytrimal.RepresentativeTrimmer attribute) R RepresentativeTrimmer (class in pytrimal) residues (pytrimal.Alignment attribute) residues_mask (pytrimal.TrimmedAlignment attribute) S sequences (pytrimal.Alignment attribute) sequences_mask (pytrimal.TrimmedAlignment attribute) similarity() (pytrimal.SimilarityMatrix method) SimilarityMatrix (class in pytrimal) T terminal_only() (pytrimal.TrimmedAlignment method) to_biopython() (pytrimal.Alignment method) to_pyhmmer() (pytrimal.Alignment method) trim() (pytrimal.AutomaticTrimmer method) (pytrimal.BaseTrimmer method) (pytrimal.ManualTrimmer method) (pytrimal.OverlapTrimmer method) (pytrimal.RepresentativeTrimmer method) TrimmedAlignment (class in pytrimal)