Index _ | A | B | C | D | E | F | G | H | I | J | K | L | M | N | O | P | Q | R | S | T | U | V | W | X | Z _ __getitem__() (pyhmmer.plan7.Traces method) __init__() (pyhmmer.daemon.Client method) (pyhmmer.daemon.IterativeSearch method) (pyhmmer.easel.Bitfield method) (pyhmmer.easel.DigitalMSA method) (pyhmmer.easel.DigitalSequence method) (pyhmmer.easel.DigitalSequenceBlock method) (pyhmmer.easel.GeneticCode method) (pyhmmer.easel.KeyHash method) (pyhmmer.easel.MatrixD method) (pyhmmer.easel.MatrixF method) (pyhmmer.easel.MatrixI method) (pyhmmer.easel.MatrixU8 method) (pyhmmer.easel.MSAFile method) (pyhmmer.easel.Randomness method) (pyhmmer.easel.SequenceFile method) (pyhmmer.easel.SSIReader method) (pyhmmer.easel.SSIWriter method) (pyhmmer.easel.TextMSA method) (pyhmmer.easel.TextSequence method) (pyhmmer.easel.TextSequenceBlock method) (pyhmmer.easel.VectorD method) (pyhmmer.easel.VectorF method) (pyhmmer.easel.VectorI method) (pyhmmer.easel.VectorU8 method) (pyhmmer.errors.AllocationError method) (pyhmmer.errors.AlphabetMismatch method) (pyhmmer.errors.EaselError method) (pyhmmer.errors.InvalidHMM method) (pyhmmer.errors.InvalidParameter method) (pyhmmer.errors.MissingCutoffs method) (pyhmmer.errors.ServerError method) (pyhmmer.errors.UnexpectedError method) (pyhmmer.plan7.Background method) (pyhmmer.plan7.Builder method) (pyhmmer.plan7.HMM method) (pyhmmer.plan7.HMMFile method) (pyhmmer.plan7.HMMPressedFile method) (pyhmmer.plan7.LongTargetsPipeline method) (pyhmmer.plan7.OptimizedProfile method) (pyhmmer.plan7.OptimizedProfileBlock method) (pyhmmer.plan7.Pipeline method) (pyhmmer.plan7.Profile method) (pyhmmer.plan7.TopHits method) (pyhmmer.plan7.Trace method) (pyhmmer.plan7.Traces method) _from_raw_bytes() (pyhmmer.easel.Matrix class method) A AA (class in pyhmmer.easel) accession (pyhmmer.easel.DigitalMSA attribute) (pyhmmer.easel.DigitalSequence attribute) (pyhmmer.easel.MSA attribute) (pyhmmer.easel.Sequence attribute) (pyhmmer.easel.TextMSA attribute) (pyhmmer.easel.TextSequence attribute) (pyhmmer.plan7.Hit attribute) (pyhmmer.plan7.HMM attribute) (pyhmmer.plan7.OptimizedProfile attribute) (pyhmmer.plan7.Profile attribute) add() (pyhmmer.easel.KeyHash method) add_alias() (pyhmmer.easel.SSIWriter method) add_file() (pyhmmer.easel.SSIWriter method) add_key() (pyhmmer.easel.SSIWriter method) align_traces() (pyhmmer.plan7.TraceAligner method) Alignment (class in pyhmmer.plan7) alignment (pyhmmer.easel.DigitalMSA attribute) (pyhmmer.easel.TextMSA attribute) (pyhmmer.plan7.Domain attribute) AllocationError allocM (pyhmmer.plan7.OptimizedProfile attribute) (pyhmmer.plan7.Profile attribute) Alphabet (class in pyhmmer.easel) alphabet (pyhmmer.easel.DigitalMSA attribute) (pyhmmer.easel.DigitalSequence attribute) (pyhmmer.easel.DigitalSequenceBlock attribute) (pyhmmer.plan7.Background attribute) (pyhmmer.plan7.Builder attribute) (pyhmmer.plan7.HMM attribute) (pyhmmer.plan7.OptimizedProfile attribute) (pyhmmer.plan7.Pipeline attribute) (pyhmmer.plan7.Profile attribute) AlphabetMismatch amino() (pyhmmer.easel.Alphabet class method) append() (pyhmmer.easel.DigitalSequenceBlock method) (pyhmmer.easel.TextSequenceBlock method) (pyhmmer.plan7.OptimizedProfileBlock method) (pyhmmer.plan7.Traces method) argmax() (pyhmmer.easel.Matrix method) (pyhmmer.easel.MatrixD method) (pyhmmer.easel.MatrixF method) (pyhmmer.easel.MatrixI method) (pyhmmer.easel.MatrixU8 method) (pyhmmer.easel.Vector method) (pyhmmer.easel.VectorD method) (pyhmmer.easel.VectorF method) (pyhmmer.easel.VectorI method) (pyhmmer.easel.VectorU8 method) argmin() (pyhmmer.easel.Matrix method) (pyhmmer.easel.MatrixD method) (pyhmmer.easel.MatrixF method) (pyhmmer.easel.MatrixI method) (pyhmmer.easel.MatrixU8 method) (pyhmmer.easel.Vector method) (pyhmmer.easel.VectorD method) (pyhmmer.easel.VectorF method) (pyhmmer.easel.VectorI method) (pyhmmer.easel.VectorU8 method) arguments() (pyhmmer.plan7.LongTargetsPipeline method) (pyhmmer.plan7.Pipeline method) as_vector() (pyhmmer.plan7.Cutoffs method) (pyhmmer.plan7.EvalueParameters method) author (pyhmmer.easel.DigitalMSA attribute) (pyhmmer.easel.MSA attribute) (pyhmmer.easel.TextMSA attribute) B B1 (pyhmmer.plan7.LongTargetsPipeline attribute) B2 (pyhmmer.plan7.LongTargetsPipeline attribute) B3 (pyhmmer.plan7.LongTargetsPipeline attribute) Background (class in pyhmmer.plan7) background (pyhmmer.plan7.Pipeline attribute) base_b (pyhmmer.plan7.OptimizedProfile attribute) base_w (pyhmmer.plan7.OptimizedProfile attribute) best_domain (pyhmmer.plan7.Hit attribute) bias (pyhmmer.plan7.Domain attribute) (pyhmmer.plan7.Hit attribute) bias_b (pyhmmer.plan7.OptimizedProfile attribute) bias_filter (pyhmmer.plan7.Pipeline attribute) bit_cutoffs (pyhmmer.plan7.Pipeline attribute) (pyhmmer.plan7.TopHits attribute) Bitfield (class in pyhmmer.easel) block_length (pyhmmer.plan7.TopHits attribute) BM (pyhmmer.plan7.ProfileTransitions attribute) build() (pyhmmer.plan7.Builder method) build_msa() (pyhmmer.plan7.Builder method) Builder (class in pyhmmer.plan7) builder (pyhmmer.daemon.IterativeSearch attribute) (pyhmmer.plan7.IterativeSearch attribute) C c_evalue (pyhmmer.plan7.Domain attribute) checksum (pyhmmer.plan7.HMM attribute) checksum() (pyhmmer.easel.DigitalMSA method) (pyhmmer.easel.DigitalSequence method) (pyhmmer.easel.MSA method) (pyhmmer.easel.Sequence method) (pyhmmer.easel.TextMSA method) (pyhmmer.easel.TextSequence method) clear() (pyhmmer.easel.DigitalSequence method) (pyhmmer.easel.DigitalSequenceBlock method) (pyhmmer.easel.KeyHash method) (pyhmmer.easel.Sequence method) (pyhmmer.easel.SequenceBlock method) (pyhmmer.easel.TextSequence method) (pyhmmer.easel.TextSequenceBlock method) (pyhmmer.plan7.OptimizedProfileBlock method) (pyhmmer.plan7.Pipeline method) (pyhmmer.plan7.Profile method) (pyhmmer.plan7.Traces method) Client (class in pyhmmer.daemon) client (pyhmmer.daemon.IterativeSearch attribute) close() (pyhmmer.daemon.Client method) (pyhmmer.easel.MSAFile method) (pyhmmer.easel.SequenceFile method) (pyhmmer.easel.SSIReader method) (pyhmmer.easel.SSIWriter method) (pyhmmer.plan7.HMMFile method) (pyhmmer.plan7.HMMPressedFile method) closed (pyhmmer.easel.MSAFile attribute) (pyhmmer.easel.SequenceFile attribute) (pyhmmer.plan7.HMMFile attribute) (pyhmmer.plan7.HMMPressedFile attribute) command_line (pyhmmer.plan7.HMM attribute) compare_ranking() (pyhmmer.plan7.TopHits method) composition (pyhmmer.plan7.HMM attribute) compositions (pyhmmer.plan7.OptimizedProfile attribute) compute_traces() (pyhmmer.plan7.TraceAligner method) compute_weights() (pyhmmer.easel.DigitalMSA method) (pyhmmer.easel.MSA method) (pyhmmer.easel.TextMSA method) configure() (pyhmmer.plan7.Profile method) connect() (pyhmmer.daemon.Client method) consensus (pyhmmer.plan7.HMM attribute) (pyhmmer.plan7.OptimizedProfile attribute) (pyhmmer.plan7.Profile attribute) consensus_accessibility (pyhmmer.plan7.HMM attribute) consensus_structure (pyhmmer.plan7.HMM attribute) (pyhmmer.plan7.OptimizedProfile attribute) (pyhmmer.plan7.Profile attribute) converged (pyhmmer.daemon.IterativeSearch attribute) (pyhmmer.plan7.IterationResult attribute) (pyhmmer.plan7.IterativeSearch attribute) convert() (pyhmmer.plan7.OptimizedProfile method) copy() (pyhmmer.easel.Bitfield method) (pyhmmer.easel.DigitalMSA method) (pyhmmer.easel.DigitalSequence method) (pyhmmer.easel.DigitalSequenceBlock method) (pyhmmer.easel.KeyHash method) (pyhmmer.easel.Matrix method) (pyhmmer.easel.MatrixD method) (pyhmmer.easel.MatrixF method) (pyhmmer.easel.MatrixI method) (pyhmmer.easel.MatrixU8 method) (pyhmmer.easel.Randomness method) (pyhmmer.easel.Sequence method) (pyhmmer.easel.SequenceBlock method) (pyhmmer.easel.TextMSA method) (pyhmmer.easel.TextSequence method) (pyhmmer.easel.TextSequenceBlock method) (pyhmmer.easel.Vector method) (pyhmmer.easel.VectorD method) (pyhmmer.easel.VectorF method) (pyhmmer.easel.VectorI method) (pyhmmer.easel.VectorU8 method) (pyhmmer.plan7.Background method) (pyhmmer.plan7.Builder method) (pyhmmer.plan7.HMM method) (pyhmmer.plan7.OptimizedProfile method) (pyhmmer.plan7.OptimizedProfileBlock method) (pyhmmer.plan7.Profile method) (pyhmmer.plan7.TopHits method) correction (pyhmmer.plan7.Domain attribute) count() (pyhmmer.easel.Bitfield method) creation_time (pyhmmer.plan7.HMM attribute) Cutoffs (class in pyhmmer.plan7) cutoffs (pyhmmer.plan7.HMM attribute) (pyhmmer.plan7.OptimizedProfile attribute) (pyhmmer.plan7.Profile attribute) D data_offset (pyhmmer.easel.SSIReader.Entry attribute) db (pyhmmer.daemon.IterativeSearch attribute) DD (pyhmmer.plan7.ProfileTransitions attribute) (pyhmmer.plan7.Transitions attribute) ddbound_w (pyhmmer.plan7.OptimizedProfile attribute) decode() (pyhmmer.easel.Alphabet method) description (pyhmmer.easel.DigitalMSA attribute) (pyhmmer.easel.DigitalSequence attribute) (pyhmmer.easel.GeneticCode attribute) (pyhmmer.easel.MSA attribute) (pyhmmer.easel.Sequence attribute) (pyhmmer.easel.TextMSA attribute) (pyhmmer.easel.TextSequence attribute) (pyhmmer.plan7.Hit attribute) (pyhmmer.plan7.HMM attribute) (pyhmmer.plan7.OptimizedProfile attribute) (pyhmmer.plan7.Profile attribute) digital (pyhmmer.easel.MSAFile attribute) (pyhmmer.easel.SequenceFile attribute) DigitalMSA (class in pyhmmer.easel) DigitalSequence (class in pyhmmer.easel) DigitalSequenceBlock (class in pyhmmer.easel) digitize() (pyhmmer.easel.TextMSA method) (pyhmmer.easel.TextSequence method) (pyhmmer.easel.TextSequenceBlock method) DM (pyhmmer.plan7.ProfileTransitions attribute) (pyhmmer.plan7.Transitions attribute) DNA (class in pyhmmer.easel) dna() (pyhmmer.easel.Alphabet class method) Domain (class in pyhmmer.plan7) domain (pyhmmer.plan7.Alignment attribute) Domains (class in pyhmmer.plan7) domains (pyhmmer.plan7.Hit attribute) domE (pyhmmer.plan7.Pipeline attribute) (pyhmmer.plan7.TopHits attribute) domT (pyhmmer.plan7.Pipeline attribute) (pyhmmer.plan7.TopHits attribute) domZ (pyhmmer.plan7.Pipeline attribute) (pyhmmer.plan7.TopHits attribute) dropped (pyhmmer.plan7.Hit attribute) duplicate (pyhmmer.plan7.Hit attribute) E E (pyhmmer.plan7.Pipeline attribute) (pyhmmer.plan7.TopHits attribute) EaselError emission_scores (pyhmmer.plan7.Profile attribute) emit_alignment() (pyhmmer.plan7.HMM method) emit_sequence() (pyhmmer.plan7.HMM method) (pyhmmer.plan7.Profile.HMM method) encode() (pyhmmer.easel.Alphabet method) entropy() (pyhmmer.easel.VectorD method) (pyhmmer.easel.VectorF method) env_from (pyhmmer.plan7.Domain attribute) env_to (pyhmmer.plan7.Domain attribute) envelope_score (pyhmmer.plan7.Domain attribute) evalue (pyhmmer.plan7.Hit attribute) evalue_parameters (pyhmmer.plan7.HMM attribute) (pyhmmer.plan7.OptimizedProfile attribute) (pyhmmer.plan7.Profile attribute) EvalueParameters (class in pyhmmer.plan7) expected_accuracy() (pyhmmer.plan7.Trace method) extend() (pyhmmer.easel.DigitalSequenceBlock method) (pyhmmer.easel.SequenceBlock method) (pyhmmer.easel.TextSequenceBlock method) (pyhmmer.plan7.OptimizedProfileBlock method) (pyhmmer.plan7.Traces method) F F1 (pyhmmer.plan7.Pipeline attribute) F2 (pyhmmer.plan7.Pipeline attribute) F3 (pyhmmer.plan7.Pipeline attribute) f_lambda (pyhmmer.plan7.EvalueParameters attribute) f_tau (pyhmmer.plan7.EvalueParameters attribute) fast (pyhmmer.easel.Randomness attribute) fd (pyhmmer.easel.SSIReader.Entry attribute) file_info() (pyhmmer.easel.SSIReader method) find_name() (pyhmmer.easel.SSIReader method) flatten() (pyhmmer.easel.Matrix method) (pyhmmer.easel.MatrixD method) (pyhmmer.easel.MatrixF method) (pyhmmer.easel.MatrixI method) (pyhmmer.easel.MatrixU8 method) format (pyhmmer.easel.Matrix attribute) (pyhmmer.easel.MatrixD attribute) (pyhmmer.easel.MatrixF attribute) (pyhmmer.easel.MatrixI attribute) (pyhmmer.easel.MatrixU8 attribute) (pyhmmer.easel.MSAFile attribute) (pyhmmer.easel.SequenceFile attribute) (pyhmmer.easel.SSIReader.FileInfo attribute) (pyhmmer.easel.Vector attribute) from_sequence() (pyhmmer.plan7.Trace class method) G gap_index (pyhmmer.easel.Alphabet attribute) gap_symbol (pyhmmer.easel.Alphabet attribute) gathering (pyhmmer.plan7.Cutoffs attribute) gathering1 (pyhmmer.plan7.Cutoffs attribute) gathering2 (pyhmmer.plan7.Cutoffs attribute) gathering_available() (pyhmmer.plan7.Cutoffs method) GeneticCode (class in pyhmmer.easel) getstate() (pyhmmer.easel.Randomness method) guess_alphabet() (pyhmmer.easel.MSAFile method) (pyhmmer.easel.SequenceFile method) H Hit (class in pyhmmer.plan7) hit (pyhmmer.plan7.Domain attribute) (pyhmmer.plan7.Domains attribute) hits (pyhmmer.plan7.IterationResult attribute) HMM (class in pyhmmer.plan7) hmm (pyhmmer.plan7.IterationResult attribute) hmm_accession (pyhmmer.plan7.Alignment attribute) hmm_from (pyhmmer.plan7.Alignment attribute) hmm_length (pyhmmer.plan7.Alignment attribute) hmm_name (pyhmmer.plan7.Alignment attribute) hmm_sequence (pyhmmer.plan7.Alignment attribute) hmm_to (pyhmmer.plan7.Alignment attribute) hmmalign() (in module pyhmmer.hmmer) HMMFile (class in pyhmmer.plan7) hmmpress() (in module pyhmmer.hmmer) HMMPressedFile (class in pyhmmer.plan7) hmmscan() (in module pyhmmer.hmmer) hmmsearch() (in module pyhmmer.hmmer) I i_evalue (pyhmmer.plan7.Domain attribute) identity_filter() (pyhmmer.easel.DigitalMSA method) identity_sequence (pyhmmer.plan7.Alignment attribute) II (pyhmmer.plan7.ProfileTransitions attribute) (pyhmmer.plan7.Transitions attribute) IM (pyhmmer.plan7.ProfileTransitions attribute) (pyhmmer.plan7.Transitions attribute) incdomE (pyhmmer.plan7.Pipeline attribute) (pyhmmer.plan7.TopHits attribute) incdomT (pyhmmer.plan7.Pipeline attribute) (pyhmmer.plan7.TopHits attribute) incE (pyhmmer.plan7.Pipeline attribute) (pyhmmer.plan7.TopHits attribute) included (pyhmmer.plan7.Domain attribute) (pyhmmer.plan7.Domains attribute) (pyhmmer.plan7.Hit attribute) (pyhmmer.plan7.TopHits attribute) incT (pyhmmer.plan7.Pipeline attribute) (pyhmmer.plan7.TopHits attribute) index() (pyhmmer.easel.DigitalSequenceBlock method) (pyhmmer.easel.TextSequenceBlock method) (pyhmmer.plan7.OptimizedProfileBlock method) (pyhmmer.plan7.Traces method) indexed (pyhmmer.easel.DigitalMSA attribute) (pyhmmer.easel.DigitalSequenceBlock attribute) (pyhmmer.easel.MSA attribute) (pyhmmer.easel.MSAFile attribute) (pyhmmer.easel.SequenceBlock attribute) (pyhmmer.easel.SequenceFile attribute) (pyhmmer.easel.TextMSA attribute) (pyhmmer.easel.TextSequenceBlock attribute) insert() (pyhmmer.easel.DigitalSequenceBlock method) (pyhmmer.easel.TextSequenceBlock method) (pyhmmer.plan7.OptimizedProfileBlock method) (pyhmmer.plan7.Traces method) insert_emissions (pyhmmer.plan7.HMM attribute) InvalidHMM InvalidParameter is_amino() (pyhmmer.easel.Alphabet method) is_dna() (pyhmmer.easel.Alphabet method) is_nucleotide() (pyhmmer.easel.Alphabet method) is_pressed() (pyhmmer.plan7.HMMFile method) is_rna() (pyhmmer.easel.Alphabet method) is_sorted() (pyhmmer.plan7.TopHits method) itemsize (pyhmmer.easel.Matrix attribute) (pyhmmer.easel.MatrixD attribute) (pyhmmer.easel.MatrixF attribute) (pyhmmer.easel.MatrixI attribute) (pyhmmer.easel.MatrixU8 attribute) (pyhmmer.easel.Vector attribute) iterate_hmm() (pyhmmer.daemon.Client method) (pyhmmer.plan7.Pipeline method) iterate_seq() (pyhmmer.daemon.Client method) (pyhmmer.plan7.Pipeline method) iteration (pyhmmer.daemon.IterativeSearch attribute) (pyhmmer.plan7.IterationResult attribute) (pyhmmer.plan7.IterativeSearch attribute) IterationResult (class in pyhmmer.plan7) IterativeSearch (class in pyhmmer.daemon) (class in pyhmmer.plan7) J jackhmmer() (in module pyhmmer.hmmer) K K (pyhmmer.easel.Alphabet attribute) KeyHash (class in pyhmmer.easel) Kp (pyhmmer.easel.Alphabet attribute) L L (pyhmmer.easel.DigitalSequence attribute) (pyhmmer.easel.Sequence attribute) (pyhmmer.easel.TextSequence attribute) (pyhmmer.plan7.Background attribute) (pyhmmer.plan7.OptimizedProfile attribute) (pyhmmer.plan7.Profile attribute) (pyhmmer.plan7.Trace attribute) largest() (pyhmmer.easel.DigitalSequenceBlock method) (pyhmmer.easel.SequenceBlock method) (pyhmmer.easel.TextSequenceBlock method) length (pyhmmer.plan7.Hit attribute) local (pyhmmer.plan7.OptimizedProfile attribute) (pyhmmer.plan7.Profile attribute) long_targets (pyhmmer.plan7.TopHits attribute) LongTargetsPipeline (class in pyhmmer.plan7) M M (pyhmmer.plan7.HMM attribute) (pyhmmer.plan7.OptimizedProfile attribute) (pyhmmer.plan7.Profile attribute) (pyhmmer.plan7.Trace attribute) m_lambda (pyhmmer.plan7.EvalueParameters attribute) m_mu (pyhmmer.plan7.EvalueParameters attribute) mark_fragments() (pyhmmer.easel.DigitalMSA method) (pyhmmer.easel.MSA method) (pyhmmer.easel.TextMSA method) match_emissions (pyhmmer.plan7.HMM attribute) match_occupancy() (pyhmmer.plan7.HMM method) Matrix (class in pyhmmer.easel) MatrixD (class in pyhmmer.easel) MatrixF (class in pyhmmer.easel) MatrixI (class in pyhmmer.easel) MatrixU8 (class in pyhmmer.easel) max() (pyhmmer.easel.Matrix method) (pyhmmer.easel.MatrixD method) (pyhmmer.easel.MatrixF method) (pyhmmer.easel.MatrixI method) (pyhmmer.easel.MatrixU8 method) (pyhmmer.easel.Vector method) (pyhmmer.easel.VectorD method) (pyhmmer.easel.VectorF method) (pyhmmer.easel.VectorI method) (pyhmmer.easel.VectorU8 method) MD (pyhmmer.plan7.ProfileTransitions attribute) (pyhmmer.plan7.Transitions attribute) mean_match_entropy() (pyhmmer.plan7.HMM method) mean_match_information() (pyhmmer.plan7.HMM method) mean_match_relative_entropy() (pyhmmer.plan7.HMM method) merge() (pyhmmer.plan7.TopHits method) MI (pyhmmer.plan7.ProfileTransitions attribute) (pyhmmer.plan7.Transitions attribute) min() (pyhmmer.easel.Matrix method) (pyhmmer.easel.MatrixD method) (pyhmmer.easel.MatrixF method) (pyhmmer.easel.MatrixI method) (pyhmmer.easel.MatrixU8 method) (pyhmmer.easel.Vector method) (pyhmmer.easel.VectorD method) (pyhmmer.easel.VectorF method) (pyhmmer.easel.VectorI method) (pyhmmer.easel.VectorU8 method) MissingCutoffs MM (pyhmmer.plan7.ProfileTransitions attribute) (pyhmmer.plan7.Transitions attribute) mode (pyhmmer.plan7.TopHits attribute) model_mask (pyhmmer.easel.DigitalMSA attribute) (pyhmmer.easel.MSA attribute) (pyhmmer.easel.TextMSA attribute) (pyhmmer.plan7.HMM attribute) (pyhmmer.plan7.OptimizedProfile attribute) module pyhmmer.daemon pyhmmer.easel pyhmmer.errors pyhmmer.hmmer pyhmmer.plan7 MSA (class in pyhmmer.easel) msa (pyhmmer.plan7.IterationResult attribute) MSAFile (class in pyhmmer.easel) msv_filter() (pyhmmer.plan7.OptimizedProfile method) (pyhmmer.plan7.Profile method) multihit (pyhmmer.plan7.OptimizedProfile attribute) (pyhmmer.plan7.Profile attribute) N name (pyhmmer.easel.DigitalMSA attribute) (pyhmmer.easel.DigitalSequence attribute) (pyhmmer.easel.MSA attribute) (pyhmmer.easel.MSAFile attribute) (pyhmmer.easel.Sequence attribute) (pyhmmer.easel.SSIReader.FileInfo attribute) (pyhmmer.easel.TextMSA attribute) (pyhmmer.easel.TextSequence attribute) (pyhmmer.plan7.Hit attribute) (pyhmmer.plan7.HMM attribute) (pyhmmer.plan7.HMMFile attribute) (pyhmmer.plan7.HMMPressedFile attribute) (pyhmmer.plan7.OptimizedProfile attribute) (pyhmmer.plan7.Profile attribute) names (pyhmmer.easel.DigitalMSA attribute) (pyhmmer.easel.MSA attribute) (pyhmmer.easel.TextMSA attribute) ncj_roundoff (pyhmmer.plan7.OptimizedProfile attribute) new (pyhmmer.plan7.Hit attribute) nhmmer() (in module pyhmmer.hmmer) noise (pyhmmer.plan7.Cutoffs attribute) noise1 (pyhmmer.plan7.Cutoffs attribute) noise2 (pyhmmer.plan7.Cutoffs attribute) noise_available() (pyhmmer.plan7.Cutoffs method) normalize() (pyhmmer.easel.VectorD method) (pyhmmer.easel.VectorF method) normalvariate() (pyhmmer.easel.Randomness method) nseq (pyhmmer.plan7.HMM attribute) nseq_effective (pyhmmer.plan7.HMM attribute) null1() (pyhmmer.plan7.Background method) null2 (pyhmmer.plan7.Pipeline attribute) O Offsets (class in pyhmmer.plan7) offsets (pyhmmer.plan7.OptimizedProfile attribute) (pyhmmer.plan7.Profile attribute) omega (pyhmmer.plan7.Background attribute) ones() (pyhmmer.easel.Bitfield class method) optimized_profiles() (pyhmmer.plan7.HMMFile method) OptimizedProfile (class in pyhmmer.plan7) OptimizedProfileBlock (class in pyhmmer.plan7) P parse() (pyhmmer.easel.MSAFile class method) (pyhmmer.easel.SequenceFile class method) parseinto() (pyhmmer.easel.SequenceFile class method) pextend (pyhmmer.plan7.Builder attribute) phmmer() (in module pyhmmer.hmmer) Pipeline (class in pyhmmer.plan7) pipeline (pyhmmer.plan7.IterativeSearch attribute) pop() (pyhmmer.easel.DigitalSequenceBlock method) (pyhmmer.easel.TextSequenceBlock method) (pyhmmer.plan7.OptimizedProfileBlock method) (pyhmmer.plan7.Traces method) popen (pyhmmer.plan7.Builder attribute) posterior_probabilities (pyhmmer.easel.DigitalMSA attribute) (pyhmmer.easel.MSA attribute) (pyhmmer.easel.TextMSA attribute) (pyhmmer.plan7.Alignment attribute) (pyhmmer.plan7.Trace attribute) pre_score (pyhmmer.plan7.Hit attribute) primary_keys (pyhmmer.easel.SSIReader attribute) Profile (class in pyhmmer.plan7) ProfileTransitions (class in pyhmmer.plan7) pvalue (pyhmmer.plan7.Domain attribute) (pyhmmer.plan7.Hit attribute) pyhmmer.daemon module pyhmmer.easel module pyhmmer.errors module pyhmmer.hmmer module pyhmmer.plan7 module Q query (pyhmmer.daemon.IterativeSearch attribute) (pyhmmer.plan7.IterativeSearch attribute) (pyhmmer.plan7.TopHits attribute) R random() (pyhmmer.easel.Randomness method) Randomness (class in pyhmmer.easel) randomness (pyhmmer.plan7.Builder attribute) (pyhmmer.plan7.Pipeline attribute) ranking (pyhmmer.daemon.IterativeSearch attribute) (pyhmmer.plan7.IterativeSearch attribute) rbv (pyhmmer.plan7.OptimizedProfile attribute) read() (pyhmmer.easel.MSAFile method) (pyhmmer.easel.SequenceFile method) (pyhmmer.plan7.HMMFile method) (pyhmmer.plan7.HMMPressedFile method) read_block() (pyhmmer.easel.SequenceFile method) readinto() (pyhmmer.easel.SequenceFile method) record_length (pyhmmer.easel.SSIReader.Entry attribute) record_offset (pyhmmer.easel.SSIReader.Entry attribute) reference (pyhmmer.easel.DigitalMSA attribute) (pyhmmer.easel.MSA attribute) (pyhmmer.easel.TextMSA attribute) (pyhmmer.plan7.HMM attribute) (pyhmmer.plan7.OptimizedProfile attribute) relative_entropy() (pyhmmer.easel.VectorD method) (pyhmmer.easel.VectorF method) remove() (pyhmmer.easel.DigitalSequenceBlock method) (pyhmmer.easel.TextSequenceBlock method) (pyhmmer.plan7.OptimizedProfileBlock method) (pyhmmer.plan7.Traces method) renormalize() (pyhmmer.plan7.HMM method) reported (pyhmmer.plan7.Domain attribute) (pyhmmer.plan7.Domains attribute) (pyhmmer.plan7.Hit attribute) (pyhmmer.plan7.TopHits attribute) residue_frequencies (pyhmmer.plan7.Background attribute) residue_markups (pyhmmer.easel.DigitalSequence attribute) (pyhmmer.easel.Sequence attribute) (pyhmmer.easel.TextSequence attribute) reverse() (pyhmmer.easel.Vector method) (pyhmmer.easel.VectorD method) (pyhmmer.easel.VectorF method) (pyhmmer.easel.VectorI method) (pyhmmer.easel.VectorU8 method) reverse_complement() (pyhmmer.easel.DigitalMSA method) (pyhmmer.easel.DigitalSequence method) (pyhmmer.easel.TextSequence method) rewind() (pyhmmer.easel.SequenceFile method) (pyhmmer.plan7.HMMFile method) (pyhmmer.plan7.HMMPressedFile method) rfv (pyhmmer.plan7.OptimizedProfile attribute) RNA (class in pyhmmer.easel) rna() (pyhmmer.easel.Alphabet class method) S sample() (pyhmmer.easel.DigitalMSA method) (pyhmmer.easel.DigitalSequence method) (pyhmmer.easel.TextSequence method) (pyhmmer.plan7.HMM method) sbv (pyhmmer.plan7.OptimizedProfile attribute) scale() (pyhmmer.plan7.HMM method) scale_b (pyhmmer.plan7.OptimizedProfile attribute) scale_w (pyhmmer.plan7.OptimizedProfile attribute) scan_seq() (pyhmmer.daemon.Client method) (pyhmmer.plan7.LongTargetsPipeline method) (pyhmmer.plan7.Pipeline method) score (pyhmmer.plan7.Domain attribute) (pyhmmer.plan7.Hit attribute) score() (pyhmmer.plan7.Trace method) score_matrix (pyhmmer.plan7.Builder attribute) search_hmm() (pyhmmer.daemon.Client method) (pyhmmer.plan7.LongTargetsPipeline method) (pyhmmer.plan7.Pipeline method) search_msa() (pyhmmer.plan7.LongTargetsPipeline method) (pyhmmer.plan7.Pipeline method) search_seq() (pyhmmer.daemon.Client method) (pyhmmer.plan7.LongTargetsPipeline method) (pyhmmer.plan7.Pipeline method) searched_models (pyhmmer.plan7.TopHits attribute) searched_nodes (pyhmmer.plan7.TopHits attribute) searched_residues (pyhmmer.plan7.TopHits attribute) searched_sequences (pyhmmer.plan7.TopHits attribute) secondary_structure (pyhmmer.easel.DigitalMSA attribute) (pyhmmer.easel.MSA attribute) (pyhmmer.easel.TextMSA attribute) seed (pyhmmer.plan7.Builder attribute) (pyhmmer.plan7.Pipeline attribute) seed() (pyhmmer.easel.Randomness method) select() (pyhmmer.easel.DigitalMSA method) (pyhmmer.easel.MSA method) (pyhmmer.easel.TextMSA method) Sequence (class in pyhmmer.easel) sequence (pyhmmer.easel.DigitalSequence attribute) (pyhmmer.easel.TextSequence attribute) sequence_weights (pyhmmer.easel.DigitalMSA attribute) (pyhmmer.easel.MSA attribute) (pyhmmer.easel.TextMSA attribute) SequenceBlock (class in pyhmmer.easel) SequenceFile (class in pyhmmer.easel) sequences (pyhmmer.easel.DigitalMSA attribute) (pyhmmer.easel.TextMSA attribute) ServerError set_composition() (pyhmmer.plan7.HMM method) set_consensus() (pyhmmer.plan7.HMM method) setstate() (pyhmmer.easel.Randomness method) shape (pyhmmer.easel.Matrix attribute) (pyhmmer.easel.Vector attribute) sort() (pyhmmer.plan7.TopHits method) source (pyhmmer.easel.DigitalSequence attribute) (pyhmmer.easel.Sequence attribute) (pyhmmer.easel.TextSequence attribute) SSIReader (class in pyhmmer.easel) SSIReader.Entry (class in pyhmmer.easel) SSIReader.FileInfo (class in pyhmmer.easel) SSIWriter (class in pyhmmer.easel) ssv_filter() (pyhmmer.plan7.OptimizedProfile method) strand (pyhmmer.plan7.Domain attribute) (pyhmmer.plan7.LongTargetsPipeline attribute) (pyhmmer.plan7.TopHits attribute) strides (pyhmmer.easel.Matrix attribute) (pyhmmer.easel.Vector attribute) sum() (pyhmmer.easel.Matrix method) (pyhmmer.easel.MatrixD method) (pyhmmer.easel.MatrixF method) (pyhmmer.easel.MatrixI method) (pyhmmer.easel.MatrixU8 method) (pyhmmer.easel.Vector method) (pyhmmer.easel.VectorD method) (pyhmmer.easel.VectorF method) (pyhmmer.easel.VectorI method) (pyhmmer.easel.VectorU8 method) sum_score (pyhmmer.plan7.Hit attribute) surface_accessibility (pyhmmer.easel.DigitalMSA attribute) (pyhmmer.easel.MSA attribute) (pyhmmer.easel.TextMSA attribute) symbols (pyhmmer.easel.Alphabet attribute) T T (pyhmmer.plan7.Pipeline attribute) (pyhmmer.plan7.TopHits attribute) target_from (pyhmmer.plan7.Alignment attribute) target_length (pyhmmer.plan7.Alignment attribute) target_name (pyhmmer.plan7.Alignment attribute) target_sequence (pyhmmer.plan7.Alignment attribute) target_to (pyhmmer.plan7.Alignment attribute) targets (pyhmmer.plan7.IterativeSearch attribute) tbm (pyhmmer.plan7.OptimizedProfile attribute) tec (pyhmmer.plan7.OptimizedProfile attribute) textize() (pyhmmer.easel.DigitalMSA method) (pyhmmer.easel.DigitalSequence method) (pyhmmer.easel.DigitalSequenceBlock method) TextMSA (class in pyhmmer.easel) TextSequence (class in pyhmmer.easel) TextSequenceBlock (class in pyhmmer.easel) tfv (pyhmmer.plan7.OptimizedProfile attribute) tjb (pyhmmer.plan7.OptimizedProfile attribute) to_msa() (pyhmmer.plan7.TopHits method) to_optimized() (pyhmmer.plan7.Profile method) to_profile() (pyhmmer.plan7.HMM method) toggle() (pyhmmer.easel.Bitfield method) TopHits (class in pyhmmer.plan7) total_length() (pyhmmer.easel.DigitalSequenceBlock method) (pyhmmer.easel.SequenceBlock method) (pyhmmer.easel.TextSequenceBlock method) Trace (class in pyhmmer.plan7) TraceAligner (class in pyhmmer.plan7) Traces (class in pyhmmer.plan7) transition_probabilities (pyhmmer.plan7.HMM attribute) transition_probability (pyhmmer.plan7.Background attribute) Transitions (class in pyhmmer.plan7) translate() (pyhmmer.easel.DigitalSequence method) (pyhmmer.easel.DigitalSequenceBlock method) (pyhmmer.easel.GeneticCode method) translation_table (pyhmmer.easel.GeneticCode attribute) trusted (pyhmmer.plan7.Cutoffs attribute) trusted1 (pyhmmer.plan7.Cutoffs attribute) trusted2 (pyhmmer.plan7.Cutoffs attribute) trusted_available() (pyhmmer.plan7.Cutoffs method) type (pyhmmer.easel.Alphabet attribute) U UnexpectedError uniform (pyhmmer.plan7.Background attribute) V v_lambda (pyhmmer.plan7.EvalueParameters attribute) v_mu (pyhmmer.plan7.EvalueParameters attribute) validate() (pyhmmer.plan7.HMM method) Vector (class in pyhmmer.easel) VectorD (class in pyhmmer.easel) VectorF (class in pyhmmer.easel) VectorI (class in pyhmmer.easel) VectorU8 (class in pyhmmer.easel) W window_beta (pyhmmer.plan7.Builder attribute) (pyhmmer.plan7.LongTargetsPipeline attribute) window_length (pyhmmer.plan7.Builder attribute) (pyhmmer.plan7.LongTargetsPipeline attribute) write() (pyhmmer.easel.DigitalMSA method) (pyhmmer.easel.DigitalSequence method) (pyhmmer.easel.DigitalSequenceBlock method) (pyhmmer.easel.MSA method) (pyhmmer.easel.Sequence method) (pyhmmer.easel.SequenceBlock method) (pyhmmer.easel.TextMSA method) (pyhmmer.easel.TextSequence method) (pyhmmer.easel.TextSequenceBlock method) (pyhmmer.plan7.HMM method) (pyhmmer.plan7.OptimizedProfile method) (pyhmmer.plan7.TopHits method) X xf (pyhmmer.plan7.OptimizedProfile attribute) Z Z (pyhmmer.plan7.Pipeline attribute) (pyhmmer.plan7.TopHits attribute) zero() (pyhmmer.plan7.HMM method) zeros() (pyhmmer.easel.Bitfield class method) (pyhmmer.easel.Matrix class method) (pyhmmer.easel.Vector class method)
