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althonos
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pyhmmer
Cython bindings and Python interface to HMMER3.
https://pyhmmer.readthedocs.io
MIT License
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Parameter to remove insert column in `hmmalign`
#74
apcamargo
opened
3 weeks ago
0
Return a single TopHits object when passing a single hmm to hmmsearch
#73
alex-hh
opened
3 weeks ago
0
"Erroneous" type warning?
#72
leoburgy
closed
1 month ago
2
PyHmmer sets CPU float behaviour globally, potentially causing issues in other libraries
#71
jakobnissen
opened
1 month ago
1
Uninformative error when input hmm file contains profiles with different alphabets
#70
Sann5
closed
2 months ago
2
BUG: `plan7.HMM.validate()` fails to raise exceptions with ill formatted hmm profiles
#69
Sann5
opened
3 months ago
1
[question] PyInfernal?
#68
tomdstanton
opened
4 months ago
3
[Bug] Pickling and unpickling an HMM object changes the cutoff values
#67
jolespin
closed
4 months ago
5
[Question] What does does `included` and `reported` mean in pyhmmer.plan7.Hit?
#66
jolespin
closed
4 months ago
2
Apply cutoffs for domains
#65
apcamargo
opened
5 months ago
2
Guess bit_cutoffs in hmmsearch
#64
jpjarnoux
opened
5 months ago
0
pyhmmer.hmmer.hmmsearch is always slower than using hmmsearch directly
#63
Gmar999
closed
5 months ago
6
`pyhmmer.nhmmer` throws error when the number of FASTA seqs is larger than 64
#62
moshi4
closed
6 months ago
2
HMMSearch block and freeze
#61
jpjarnoux
closed
6 months ago
5
Hmmsearch callback tqdm update
#60
jpjarnoux
closed
6 months ago
4
Expose ppline in Alignment class
#59
arajkovic
closed
6 months ago
3
cannot reproduce example for ```pyhmmer.hmmer.hmmsearch```
#58
erfanshekarriz
opened
9 months ago
1
[Feature Request] Internally assigning Z for ```HMM``` class
#57
erfanshekarriz
opened
9 months ago
3
Save the DigitalSequenceBlock as pickle
#56
chtsai0105
closed
10 months ago
6
Scoring a set of sequences with HMM
#55
paoslaos
closed
10 months ago
3
Added new publication to the .rst
#54
halanzi
closed
11 months ago
1
`hmmscan` gets confused about short monotone sequences' alphabet. ( assumes `Amino`, actually `RNA`)
#53
rtviii
closed
11 months ago
7
Update plan7.pyx
#52
rtviii
closed
11 months ago
2
Batch the hmmsearch output
#51
chtsai0105
closed
1 year ago
5
Aborted (core dumped) occurred while doing translate
#50
chtsai0105
closed
1 year ago
3
Best way to Read in/Search Over Many Many HMMs?
#49
gbouras13
closed
1 year ago
3
Load more than 1024 HMM files
#48
chtsai0105
closed
1 year ago
2
De-increment nincluded/nreported after merge
#47
zdk123
closed
1 year ago
10
Reported/Included domain counts are doubled after TopHits merge
#46
zdk123
closed
1 year ago
2
Production stable or WIP
#45
oschwengers
opened
1 year ago
1
PyHmmer installation error
#44
RSweeney25
closed
1 year ago
1
`incE` not being respected
#43
EvanKomp
closed
1 year ago
2
Error while running nhmmer
#42
theabhirath
closed
1 year ago
3
CPUs not being utilized
#41
EvanKomp
closed
1 year ago
8
PyHMMER 0.8.0 TMD should be 0 for last node
#40
jamaliki
closed
1 year ago
5
Generating sequences
#39
mireklzicar
closed
1 year ago
1
Conflict with numba
#38
seanrjohnson
closed
3 months ago
3
Error raised from C code: fseeko() failed, eslESYS (status code 12)
#37
k-krakowski
closed
1 year ago
1
segmentation fault in hmmalign
#36
ChristophKnapp
closed
1 year ago
8
Proposal to add `pyhmmer.jackhmmer` function
#35
zdk123
closed
1 year ago
5
Fix iterate hmm
#34
zdk123
closed
1 year ago
6
Query type is mis-specified in `iterate_hmm`
#33
zdk123
closed
1 year ago
0
search_hmm with --cut-ga
#32
willhuynh11
closed
1 year ago
2
Save sequence name after translation
#31
valentynbez
closed
1 year ago
10
Pass query name to translated sequences
#30
valentynbez
closed
1 year ago
0
Bioconda update to v0.7.0 is blocked
#29
jhahnfeld
closed
1 year ago
3
Suggestion: Add esl-reformat as method to convert MSA to stockholm format
#28
jpjarnoux
closed
1 year ago
4
Possibility to filter alignment results on coverage between HMM and target
#27
jpjarnoux
opened
1 year ago
6
hmmsearch gathering/trusted/noise cutoffs doesn't apply to single domains (i.e., --domT)
#26
satriaphd
closed
1 year ago
4
search_hmm results in segmentation fault
#25
snerligit
closed
2 years ago
2
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