pyhmmer
0.10.11
GitHub
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Documentation
Installation
Examples
Performance
Contributing
Publications
Benchmarks
API Reference
Changelog
Index
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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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J
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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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Q
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R
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T
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V
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W
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Z
_
__copy__() (pyhmmer.easel.Bitfield method)
(pyhmmer.easel.KeyHash method)
(pyhmmer.easel.Matrix method)
(pyhmmer.easel.MSA method)
(pyhmmer.easel.Randomness method)
(pyhmmer.easel.Sequence method)
(pyhmmer.easel.SequenceBlock method)
(pyhmmer.easel.Vector method)
(pyhmmer.plan7.Background method)
(pyhmmer.plan7.Builder method)
(pyhmmer.plan7.Cutoffs method)
(pyhmmer.plan7.EvalueParameters method)
(pyhmmer.plan7.HMM method)
(pyhmmer.plan7.Offsets method)
(pyhmmer.plan7.OptimizedProfile method)
(pyhmmer.plan7.OptimizedProfileBlock method)
(pyhmmer.plan7.Profile method)
(pyhmmer.plan7.TopHits method)
__deepcopy__() (pyhmmer.easel.Bitfield method)
(pyhmmer.plan7.HMM method)
(pyhmmer.plan7.OptimizedProfile method)
(pyhmmer.plan7.Profile method)
(pyhmmer.plan7.TopHits method)
__enter__() (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)
__eq__() (pyhmmer.errors.AlphabetMismatch method)
__exit__() (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)
__getstate__() (pyhmmer.easel.Bitfield method)
(pyhmmer.easel.KeyHash method)
(pyhmmer.easel.Randomness method)
(pyhmmer.plan7.Alignment method)
(pyhmmer.plan7.Domain method)
(pyhmmer.plan7.Hit method)
(pyhmmer.plan7.HMM method)
(pyhmmer.plan7.TopHits 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.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.TextSequenceBlock method)
(pyhmmer.easel.VectorF 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.IterativeSearch 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)
__reduce__() (pyhmmer.easel.Alphabet method)
(pyhmmer.easel.DigitalSequence method)
(pyhmmer.easel.DigitalSequenceBlock method)
(pyhmmer.easel.GeneticCode method)
(pyhmmer.easel.Randomness method)
(pyhmmer.easel.SequenceBlock method)
(pyhmmer.easel.TextSequence method)
(pyhmmer.easel.TextSequenceBlock method)
(pyhmmer.plan7.Background method)
(pyhmmer.plan7.HMM method)
(pyhmmer.plan7.OptimizedProfileBlock method)
(pyhmmer.plan7.TopHits method)
__reduce_cython__() (pyhmmer.daemon.Client method)
(pyhmmer.daemon.IterativeSearch method)
(pyhmmer.plan7.IterativeSearch method)
__reduce_ex__() (pyhmmer.easel.Bitfield method)
(pyhmmer.easel.Matrix method)
(pyhmmer.easel.Vector method)
__repr__() (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)
__setstate__() (pyhmmer.easel.Bitfield method)
(pyhmmer.easel.KeyHash method)
(pyhmmer.easel.Randomness method)
(pyhmmer.plan7.Alignment method)
(pyhmmer.plan7.Domain method)
(pyhmmer.plan7.Hit method)
(pyhmmer.plan7.HMM method)
(pyhmmer.plan7.TopHits method)
__setstate_cython__() (pyhmmer.daemon.Client method)
(pyhmmer.daemon.IterativeSearch method)
(pyhmmer.plan7.IterativeSearch method)
__sizeof__() (pyhmmer.easel.Alphabet method)
(pyhmmer.easel.Bitfield method)
(pyhmmer.easel.KeyHash method)
(pyhmmer.easel.Matrix method)
(pyhmmer.easel.Randomness method)
(pyhmmer.easel.Sequence method)
(pyhmmer.easel.SequenceBlock method)
(pyhmmer.easel.Vector method)
(pyhmmer.plan7.Alignment method)
(pyhmmer.plan7.HMM method)
(pyhmmer.plan7.OptimizedProfile method)
(pyhmmer.plan7.OptimizedProfileBlock method)
(pyhmmer.plan7.Profile method)
__str__() (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)
_from_raw_bytes() (pyhmmer.easel.Bitfield class method)
(pyhmmer.easel.Matrix class method)
(pyhmmer.easel.Vector class method)
_search_hmm() (pyhmmer.daemon.IterativeSearch method)
(pyhmmer.plan7.IterativeSearch 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.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)
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)
arguments() (pyhmmer.plan7.LongTargetsPipeline method)
(pyhmmer.plan7.Pipeline 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)
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)
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.MSA method)
(pyhmmer.easel.Sequence method)
clear() (pyhmmer.easel.KeyHash method)
(pyhmmer.easel.Sequence method)
(pyhmmer.easel.SequenceBlock method)
(pyhmmer.plan7.OptimizedProfileBlock method)
(pyhmmer.plan7.Pipeline method)
(pyhmmer.plan7.Profile 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)
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.MatrixF 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.VectorF 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.Transitions attribute)
ddbound_w (pyhmmer.plan7.OptimizedProfile attribute)
decode() (pyhmmer.easel.Alphabet method)
description (pyhmmer.easel.GeneticCode attribute)
(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)
DigitalSequenceBlock (class in pyhmmer.easel)
digitize() (pyhmmer.easel.TextMSA method)
(pyhmmer.easel.TextSequence method)
(pyhmmer.easel.TextSequenceBlock method)
DM (pyhmmer.plan7.Transitions attribute)
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
encode() (pyhmmer.easel.Alphabet method)
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)
extend() (pyhmmer.easel.SequenceBlock method)
(pyhmmer.plan7.OptimizedProfileBlock 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)
format (pyhmmer.easel.Matrix attribute)
(pyhmmer.easel.MatrixF attribute)
(pyhmmer.easel.MatrixU8 attribute)
(pyhmmer.easel.MSAFile attribute)
(pyhmmer.easel.SequenceFile attribute)
(pyhmmer.easel.SSIReader.FileInfo attribute)
(pyhmmer.easel.Vector attribute)
(pyhmmer.easel.VectorF attribute)
(pyhmmer.easel.VectorU8 attribute)
from_sequence() (pyhmmer.plan7.Trace class method)
G
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_sequence (pyhmmer.plan7.Alignment attribute)
II (pyhmmer.plan7.Transitions attribute)
IM (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)
insert() (pyhmmer.easel.DigitalSequenceBlock method)
(pyhmmer.easel.TextSequenceBlock method)
(pyhmmer.plan7.OptimizedProfileBlock 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.MatrixF attribute)
(pyhmmer.easel.MatrixU8 attribute)
(pyhmmer.easel.Vector attribute)
(pyhmmer.easel.VectorF attribute)
(pyhmmer.easel.VectorU8 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.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)
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)
MD (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.Transitions attribute)
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)
MissingCutoffs
MM (pyhmmer.plan7.Transitions attribute)
mode (pyhmmer.plan7.TopHits attribute)
model_mask (pyhmmer.plan7.HMM attribute)
(pyhmmer.plan7.OptimizedProfile attribute)
module
pyhmmer
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)
multihit (pyhmmer.plan7.OptimizedProfile attribute)
(pyhmmer.plan7.Profile attribute)
N
name (pyhmmer.easel.MSA attribute)
(pyhmmer.easel.MSAFile attribute)
(pyhmmer.easel.Sequence attribute)
(pyhmmer.easel.SSIReader.FileInfo 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.MSA 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.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)
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.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)
popen (pyhmmer.plan7.Builder attribute)
posterior_probabilities (pyhmmer.plan7.Alignment attribute)
(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.daemon
module
pyhmmer.easel
module
pyhmmer.errors
module
pyhmmer.hmmer
module
pyhmmer.plan7
module
Q
query (pyhmmer.daemon.IterativeSearch attribute)
(pyhmmer.plan7.IterativeSearch attribute)
query_accession (pyhmmer.plan7.TopHits attribute)
query_length (pyhmmer.plan7.TopHits attribute)
query_name (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.plan7.HMM attribute)
(pyhmmer.plan7.OptimizedProfile attribute)
relative_entropy() (pyhmmer.easel.VectorF method)
remove() (pyhmmer.easel.DigitalSequenceBlock method)
(pyhmmer.easel.TextSequenceBlock method)
(pyhmmer.plan7.OptimizedProfileBlock 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.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)
rewind() (pyhmmer.easel.SequenceFile method)
(pyhmmer.plan7.HMMFile method)
(pyhmmer.plan7.HMMPressedFile method)
rfv (pyhmmer.plan7.OptimizedProfile attribute)
rna() (pyhmmer.easel.Alphabet class method)
S
sample() (pyhmmer.plan7.HMM class 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.plan7.LongTargetsPipeline attribute)
(pyhmmer.plan7.Pipeline attribute)
scan_seq() (pyhmmer.daemon.Client method)
score (pyhmmer.plan7.Domain attribute)
(pyhmmer.plan7.Hit attribute)
score() (pyhmmer.plan7.Trace method)
score_matrix (pyhmmer.plan7.Builder attribute)
search_hmm (pyhmmer.plan7.LongTargetsPipeline attribute)
(pyhmmer.plan7.Pipeline attribute)
search_hmm() (pyhmmer.daemon.Client 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)
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)
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.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.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.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_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)
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)
VectorF (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.MSA method)
(pyhmmer.easel.Sequence 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)