Index

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__init__() (pytrimal.Alignment method) (pytrimal.AutomaticTrimmer method) (pytrimal.BaseTrimmer method) (pytrimal.ManualTrimmer method) (pytrimal.SimilarityMatrix method) (pytrimal.TrimmedAlignment method)

A

aa() (pytrimal.SimilarityMatrix method) Alignment (class in pytrimal)

AlignmentResidues (class in pytrimal) AlignmentSequences (class in pytrimal) AutomaticTrimmer (class in pytrimal)

B

backend (pytrimal.AutomaticTrimmer attribute) (pytrimal.BaseTrimmer attribute) (pytrimal.ManualTrimmer attribute)

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)

R

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) TrimmedAlignment (class in pytrimal)