pyhmmer
0.5.0
GitHub
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PyPI
Documentation
Installation
Examples
Performance
Contributing
API Reference
Benchmarks
Changelog
Index
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A
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B
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C
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D
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E
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F
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G
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H
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I
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K
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L
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M
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N
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O
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P
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R
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S
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T
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U
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V
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W
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Z
_
__init__() (pyhmmer.easel.Bitfield method)
(pyhmmer.easel.DigitalMSA method)
(pyhmmer.easel.DigitalSequence method)
(pyhmmer.easel.KeyHash method)
(pyhmmer.easel.MatrixF 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.VectorF method)
(pyhmmer.easel.VectorU8 method)
(pyhmmer.plan7.Background method)
(pyhmmer.plan7.Builder method)
(pyhmmer.plan7.HMM method)
(pyhmmer.plan7.HMMFile method)
(pyhmmer.plan7.LongTargetsPipeline method)
(pyhmmer.plan7.OptimizedProfile method)
(pyhmmer.plan7.Pipeline method)
(pyhmmer.plan7.PipelineSearchTargets method)
(pyhmmer.plan7.Profile method)
(pyhmmer.plan7.TopHits method)
A
accession (pyhmmer.easel.MSA attribute)
(pyhmmer.easel.Sequence 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.TextMSA attribute)
(pyhmmer.plan7.Domain attribute)
AllocationError
Alphabet (class in pyhmmer.easel)
alphabet (pyhmmer.easel.DigitalMSA attribute)
(pyhmmer.easel.DigitalSequence attribute)
(pyhmmer.plan7.Background attribute)
(pyhmmer.plan7.Builder attribute)
(pyhmmer.plan7.HMM attribute)
(pyhmmer.plan7.OptimizedProfile attribute)
(pyhmmer.plan7.Pipeline attribute)
(pyhmmer.plan7.PipelineSearchTargets attribute)
(pyhmmer.plan7.Profile attribute)
AlphabetMismatch
amino() (pyhmmer.easel.Alphabet method)
argmax() (pyhmmer.easel.Matrix method)
(pyhmmer.easel.MatrixF method)
(pyhmmer.easel.MatrixU8 method)
(pyhmmer.easel.Vector method)
(pyhmmer.easel.VectorF method)
(pyhmmer.easel.VectorU8 method)
argmin() (pyhmmer.easel.Matrix method)
(pyhmmer.easel.MatrixF method)
(pyhmmer.easel.MatrixU8 method)
(pyhmmer.easel.Vector method)
(pyhmmer.easel.VectorF method)
(pyhmmer.easel.VectorU8 method)
as_vector() (pyhmmer.plan7.Cutoffs method)
(pyhmmer.plan7.EvalueParameters method)
author (pyhmmer.easel.MSA 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)
best_domain (pyhmmer.plan7.Hit attribute)
bias (pyhmmer.plan7.Domain attribute)
(pyhmmer.plan7.Hit attribute)
(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)
build() (pyhmmer.plan7.Builder method)
build_msa() (pyhmmer.plan7.Builder method)
Builder (class in pyhmmer.plan7)
C
c_evalue (pyhmmer.plan7.Domain attribute)
checksum (pyhmmer.plan7.HMM attribute)
checksum() (pyhmmer.easel.MSA method)
(pyhmmer.easel.Sequence method)
clear() (pyhmmer.easel.KeyHash method)
(pyhmmer.easel.Sequence method)
(pyhmmer.plan7.Pipeline method)
(pyhmmer.plan7.Profile method)
close() (pyhmmer.easel.MSAFile method)
(pyhmmer.easel.SequenceFile method)
(pyhmmer.easel.SSIReader method)
(pyhmmer.easel.SSIWriter method)
(pyhmmer.plan7.HMMFile method)
closed (pyhmmer.easel.MSAFile attribute)
(pyhmmer.easel.SequenceFile attribute)
(pyhmmer.plan7.HMMFile attribute)
command_line (pyhmmer.plan7.HMM attribute)
composition (pyhmmer.plan7.HMM attribute)
compute_traces() (pyhmmer.plan7.TraceAligner method)
configure() (pyhmmer.plan7.Profile 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)
convert() (pyhmmer.plan7.OptimizedProfile method)
copy() (pyhmmer.easel.DigitalMSA method)
(pyhmmer.easel.DigitalSequence method)
(pyhmmer.easel.KeyHash method)
(pyhmmer.easel.Matrix method)
(pyhmmer.easel.MatrixF method)
(pyhmmer.easel.MatrixU8 method)
(pyhmmer.easel.Randomness method)
(pyhmmer.easel.Sequence method)
(pyhmmer.easel.TextMSA method)
(pyhmmer.easel.TextSequence method)
(pyhmmer.easel.Vector method)
(pyhmmer.easel.VectorF method)
(pyhmmer.easel.VectorU8 method)
(pyhmmer.plan7.Background method)
(pyhmmer.plan7.Builder method)
(pyhmmer.plan7.HMM method)
(pyhmmer.plan7.OptimizedProfile 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 property)
description (pyhmmer.easel.MSA attribute)
(pyhmmer.easel.Sequence 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)
digitize() (pyhmmer.easel.TextMSA method)
(pyhmmer.easel.TextSequence method)
dna() (pyhmmer.easel.Alphabet 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)
E
E (pyhmmer.plan7.Pipeline attribute)
(pyhmmer.plan7.TopHits attribute)
EaselError
entropy() (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)
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)
fd() (pyhmmer.easel.SSIReader.Entry property)
file_info() (pyhmmer.easel.SSIReader method)
find_name() (pyhmmer.easel.SSIReader method)
format (pyhmmer.easel.Matrix attribute)
(pyhmmer.easel.MatrixF attribute)
(pyhmmer.easel.MatrixU8 attribute)
(pyhmmer.easel.Vector attribute)
(pyhmmer.easel.VectorF attribute)
(pyhmmer.easel.VectorU8 attribute)
format() (pyhmmer.easel.SSIReader.FileInfo property)
G
gathering (pyhmmer.plan7.Cutoffs attribute)
gathering1 (pyhmmer.plan7.Cutoffs attribute)
gathering2 (pyhmmer.plan7.Cutoffs attribute)
gathering_available() (pyhmmer.plan7.Cutoffs method)
getstate() (pyhmmer.easel.Randomness method)
H
Hit (class in pyhmmer.plan7)
hit (pyhmmer.plan7.Domain attribute)
(pyhmmer.plan7.Domains attribute)
hits_included (pyhmmer.plan7.TopHits attribute)
hits_reported (pyhmmer.plan7.TopHits attribute)
HMM (class in pyhmmer.plan7)
hmm_accession (pyhmmer.plan7.Alignment attribute)
hmm_from (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)
hmmsearch() (in module pyhmmer.hmmer)
I
i_evalue (pyhmmer.plan7.Domain attribute)
identity_sequence (pyhmmer.plan7.Alignment 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)
incT (pyhmmer.plan7.Pipeline attribute)
(pyhmmer.plan7.TopHits attribute)
insert_emissions (pyhmmer.plan7.HMM attribute)
is_amino() (pyhmmer.easel.Alphabet method)
is_dna() (pyhmmer.easel.Alphabet method)
is_dropped() (pyhmmer.plan7.Hit method)
is_duplicate() (pyhmmer.plan7.Hit method)
is_fast() (pyhmmer.easel.Randomness method)
is_included() (pyhmmer.plan7.Hit method)
is_local() (pyhmmer.plan7.OptimizedProfile method)
(pyhmmer.plan7.Profile method)
is_multihit() (pyhmmer.plan7.Profile method)
is_new() (pyhmmer.plan7.Hit method)
is_nucleotide() (pyhmmer.easel.Alphabet method)
is_pressed() (pyhmmer.plan7.HMMFile method)
is_reported() (pyhmmer.plan7.Hit method)
is_rna() (pyhmmer.easel.Alphabet method)
is_sorted() (pyhmmer.plan7.TopHits method)
itemsize (pyhmmer.easel.Matrix attribute)
(pyhmmer.easel.MatrixF attribute)
(pyhmmer.easel.MatrixU8 attribute)
(pyhmmer.easel.Vector attribute)
(pyhmmer.easel.VectorF attribute)
(pyhmmer.easel.VectorU8 attribute)
K
K (pyhmmer.easel.Alphabet attribute)
KeyHash (class in pyhmmer.easel)
Kp (pyhmmer.easel.Alphabet attribute)
L
L (pyhmmer.plan7.Background attribute)
(pyhmmer.plan7.OptimizedProfile attribute)
(pyhmmer.plan7.Profile attribute)
(pyhmmer.plan7.Trace 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)
match_emissions (pyhmmer.plan7.HMM attribute)
match_occupancy() (pyhmmer.plan7.HMM method)
Matrix (class in pyhmmer.easel)
MatrixF (class in pyhmmer.easel)
MatrixU8 (class in pyhmmer.easel)
max() (pyhmmer.easel.Matrix method)
(pyhmmer.easel.MatrixF method)
(pyhmmer.easel.MatrixU8 method)
(pyhmmer.easel.Vector method)
(pyhmmer.easel.VectorF method)
(pyhmmer.easel.VectorU8 method)
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)
min() (pyhmmer.easel.Matrix method)
(pyhmmer.easel.MatrixF method)
(pyhmmer.easel.MatrixU8 method)
(pyhmmer.easel.Vector method)
(pyhmmer.easel.VectorF method)
(pyhmmer.easel.VectorU8 method)
model_mask (pyhmmer.plan7.HMM attribute)
module
pyhmmer
pyhmmer.easel
pyhmmer.errors
pyhmmer.hmmer
pyhmmer.plan7
MSA (class in pyhmmer.easel)
MSAFile (class in pyhmmer.easel)
N
name (pyhmmer.easel.MSA attribute)
(pyhmmer.easel.Sequence attribute)
(pyhmmer.plan7.Hit attribute)
(pyhmmer.plan7.HMM attribute)
(pyhmmer.plan7.OptimizedProfile attribute)
(pyhmmer.plan7.Profile attribute)
name() (pyhmmer.easel.SSIReader.FileInfo property)
names (pyhmmer.easel.MSA 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.VectorF method)
normalvariate() (pyhmmer.easel.Randomness method)
nseq (pyhmmer.plan7.HMM attribute)
nseq_effective (pyhmmer.plan7.HMM attribute)
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)
optimized() (pyhmmer.plan7.Profile method)
optimized_profiles() (pyhmmer.plan7.HMMFile method)
OptimizedProfile (class in pyhmmer.plan7)
P
parse() (pyhmmer.easel.SequenceFile method)
parseinto() (pyhmmer.easel.SequenceFile method)
pextend (pyhmmer.plan7.Builder attribute)
phmmer() (in module pyhmmer.hmmer)
Pipeline (class in pyhmmer.plan7)
PipelineSearchTargets (class in pyhmmer.plan7)
popen (pyhmmer.plan7.Builder attribute)
posterior_probabilities (pyhmmer.plan7.Trace attribute)
pre_score (pyhmmer.plan7.Hit attribute)
Profile (class in pyhmmer.plan7)
pvalue (pyhmmer.plan7.Domain attribute)
(pyhmmer.plan7.Hit attribute)
pyhmmer
module
pyhmmer.easel
module
pyhmmer.errors
module
pyhmmer.hmmer
module
pyhmmer.plan7
module
R
random() (pyhmmer.easel.Randomness method)
Randomness (class in pyhmmer.easel)
randomness (pyhmmer.plan7.Builder attribute)
(pyhmmer.plan7.Pipeline attribute)
rbv (pyhmmer.plan7.OptimizedProfile attribute)
read() (pyhmmer.easel.MSAFile method)
(pyhmmer.easel.SequenceFile method)
(pyhmmer.plan7.HMMFile method)
readinto() (pyhmmer.easel.SequenceFile method)
record_length() (pyhmmer.easel.SSIReader.Entry property)
record_offset() (pyhmmer.easel.SSIReader.Entry property)
reference (pyhmmer.plan7.HMM attribute)
relative_entropy() (pyhmmer.easel.VectorF method)
renormalize() (pyhmmer.plan7.HMM method)
residue_frequencies (pyhmmer.plan7.Background attribute)
residue_markups (pyhmmer.easel.Sequence attribute)
reverse() (pyhmmer.easel.Vector method)
(pyhmmer.easel.VectorF method)
(pyhmmer.easel.VectorU8 method)
reverse_complement() (pyhmmer.easel.DigitalSequence method)
(pyhmmer.easel.TextSequence method)
rna() (pyhmmer.easel.Alphabet method)
S
sbv (pyhmmer.plan7.OptimizedProfile attribute)
scale() (pyhmmer.plan7.HMM method)
scan_seq() (pyhmmer.plan7.LongTargetsPipeline method)
(pyhmmer.plan7.Pipeline method)
score (pyhmmer.plan7.Domain attribute)
(pyhmmer.plan7.Hit attribute)
score_matrix (pyhmmer.plan7.Builder attribute)
search_hmm() (pyhmmer.plan7.LongTargetsPipeline method)
(pyhmmer.plan7.Pipeline method)
search_msa() (pyhmmer.plan7.LongTargetsPipeline method)
(pyhmmer.plan7.Pipeline method)
search_seq() (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)
seed (pyhmmer.plan7.Builder attribute)
(pyhmmer.plan7.Pipeline attribute)
seed() (pyhmmer.easel.Randomness method)
Sequence (class in pyhmmer.easel)
sequence (pyhmmer.easel.DigitalSequence attribute)
(pyhmmer.easel.TextSequence attribute)
SequenceFile (class in pyhmmer.easel)
sequences (pyhmmer.easel.DigitalMSA attribute)
(pyhmmer.easel.TextMSA attribute)
set_composition() (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.Sequence 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.LongTargetsPipeline attribute)
(pyhmmer.plan7.TopHits attribute)
strides (pyhmmer.easel.Matrix attribute)
(pyhmmer.easel.Vector attribute)
sum() (pyhmmer.easel.Matrix method)
(pyhmmer.easel.MatrixF method)
(pyhmmer.easel.MatrixU8 method)
(pyhmmer.easel.Vector method)
(pyhmmer.easel.VectorF method)
(pyhmmer.easel.VectorU8 method)
sum_score (pyhmmer.plan7.Hit attribute)
symbols (pyhmmer.easel.Alphabet attribute)
T
T (pyhmmer.plan7.Pipeline attribute)
(pyhmmer.plan7.TopHits attribute)
target_from (pyhmmer.plan7.Alignment attribute)
target_name (pyhmmer.plan7.Alignment attribute)
target_sequence (pyhmmer.plan7.Alignment attribute)
target_to (pyhmmer.plan7.Alignment attribute)
taxonomy_id (pyhmmer.easel.Sequence attribute)
tbm (pyhmmer.plan7.OptimizedProfile attribute)
tec (pyhmmer.plan7.OptimizedProfile attribute)
textize() (pyhmmer.easel.DigitalMSA method)
(pyhmmer.easel.DigitalSequence method)
TextMSA (class in pyhmmer.easel)
TextSequence (class in pyhmmer.easel)
tjb (pyhmmer.plan7.OptimizedProfile attribute)
to_msa() (pyhmmer.plan7.TopHits method)
toggle() (pyhmmer.easel.Bitfield method)
TopHits (class in pyhmmer.plan7)
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)
trusted (pyhmmer.plan7.Cutoffs attribute)
trusted1 (pyhmmer.plan7.Cutoffs attribute)
trusted2 (pyhmmer.plan7.Cutoffs attribute)
trusted_available() (pyhmmer.plan7.Cutoffs method)
U
UnexpectedError
uniform (pyhmmer.plan7.Background attribute)
V
v_lambda (pyhmmer.plan7.EvalueParameters attribute)
v_mu (pyhmmer.plan7.EvalueParameters attribute)
Vector (class in pyhmmer.easel)
VectorF (class in pyhmmer.easel)
VectorU8 (class in pyhmmer.easel)
W
window_beta (pyhmmer.plan7.Builder attribute)
window_length (pyhmmer.plan7.Builder attribute)
write() (pyhmmer.easel.MSA method)
(pyhmmer.easel.Sequence method)
(pyhmmer.plan7.HMM method)
(pyhmmer.plan7.OptimizedProfile method)
Z
Z (pyhmmer.plan7.Pipeline attribute)
(pyhmmer.plan7.TopHits attribute)
zero() (pyhmmer.plan7.HMM method)
zeros() (pyhmmer.easel.Matrix method)
(pyhmmer.easel.Vector method)