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filip-husnik
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pseudofinder
Detection of pseudogene candidates in bacterial and archaeal genomes.
GNU General Public License v3.0
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Some questions about dn/ds
#64
LRH1995
opened
2 months ago
0
Log file numbers do not match the description.
#63
Methanoutput
opened
2 months ago
0
Using Eggnog Mapper Annotation (Prodigal) with Pseudofinder.
#62
Methanoutput
closed
3 months ago
0
Explanation of "no_mercy" in sleuth output
#61
zakisaati
opened
10 months ago
2
Getting error TypeError: unhashable type: 'SeqFeature'
#60
nachodeq
opened
11 months ago
1
Database selection drastically changes pseudogenes reported
#59
VishnuRaghuram94
opened
1 year ago
0
`manage_blast_db` does not allow for multiple nr "volumes"
#58
dr-joe-wirth
opened
1 year ago
1
added a name for the conda environment
#57
dr-joe-wirth
opened
1 year ago
2
Sequences categorized into types of pseudogenes
#56
navkahlon240
opened
1 year ago
3
Can Pseudofinder identify pseudogenes in eukaryotic genomes?
#55
JeffreyNIEgithub
closed
1 year ago
1
Can Pseudofinder identify pseudogenes in eukaryotic genomes?
#54
JeffreyNIEgithub
closed
1 year ago
1
refseq blastdb
#53
schmittel
closed
1 year ago
1
False Postive with known complete gene
#52
LijMeh
closed
1 year ago
4
Annotate module
#51
navkahlon240
closed
1 year ago
3
Output log file
#50
navkahlon240
closed
1 year ago
1
Error running with diamond database
#49
longleyr
closed
2 years ago
2
Pseudofinder sleuth is stuck on psl2aln
#48
tandb92
closed
2 years ago
1
Bug with -ce flag
#47
liamfriar
closed
2 years ago
2
are prodigal, parallel, `pal2aln`, `hmmer` required.
#46
EricDeveaud
opened
2 years ago
0
python :: ensure intrerpreter to use
#45
EricDeveaud
closed
2 years ago
5
problem with diamond
#44
EricDeveaud
closed
2 years ago
1
pseudofinder.py test -db /X/Y/Z should not create result directory in same location of test data
#43
EricDeveaud
closed
2 years ago
3
error when no db index available
#42
EricDeveaud
closed
2 years ago
1
nr database deletion
#41
GraessleT
closed
2 years ago
5
Error when running visualize
#40
pyongheng
closed
2 years ago
1
database
#39
vappiah
closed
2 years ago
3
Sleuth error with specific reference genome
#38
pyongheng
closed
2 years ago
2
Pseudogene Names/Annotations
#37
ddf37
closed
2 years ago
3
PseudoType.Input.value.indel
#36
happykhan
closed
2 years ago
1
Sleuth.dnd
#35
fasemoreakinyemi
closed
2 years ago
1
Sleuth input files
#34
rhyman8
closed
2 years ago
4
AttributeError: module 'modules' has no attribute 'selection'?
#33
XinTongx
closed
2 years ago
2
Missing sleuth outputs
#32
rhyman8
closed
2 years ago
9
Potential duplicate locus tags detected in genome
#31
rhyman8
closed
2 years ago
2
Pseudogenes at contig edges
#30
gavinmdouglas
closed
2 years ago
2
Question regarding database format/retrieval
#29
guillemmasfiol
closed
2 years ago
2
Confidence score / database suggestion?
#28
gavinmdouglas
closed
2 years ago
10
Reportlab Module
#27
ddf37
closed
2 years ago
15
Reportlab Module Issue
#26
ddf37
closed
2 years ago
2
Output gff issues
#25
treitlis
closed
2 years ago
4
running sleuth module
#24
eddykay310
closed
2 years ago
2
Is it possible to annotate the pseudogenes out using database?
#23
ylifc
closed
2 years ago
1
running on shotgun metagenomes + difference between --length_pseudo and --perc_cov
#22
Jigyasa3
closed
2 years ago
3
dnds analysis with ref .gbff
#21
eddykay310
closed
2 years ago
15
Make Pseudofinder as a conda package
#20
ireneortega
opened
3 years ago
3
RuntimeError
#19
sarah872
closed
3 years ago
6
error with test
#18
vacatkoV
closed
3 years ago
3
Questions regarding pseudo-finder test
#17
junwkim42
closed
3 years ago
3
How to solve it?
#16
life333
closed
3 years ago
10
TypeError: can only concatenate str (not "NoneType") to str
#15
dustin-dial
closed
4 years ago
3
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