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MorrellLAB
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BAD_Mutations
Deleterious mutation prediction pipeline
MIT License
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BUG:
#54
sunshichao0916
closed
3 years ago
3
Compile - include SNP names?
#53
conJUSTover
opened
4 years ago
1
Compile Bug - Won't work on test data
#52
conJUSTover
opened
4 years ago
5
Dev
#51
TomJKono
closed
4 years ago
0
The XML document has moved
#50
hubner-lab
opened
4 years ago
2
Fetch only the latest CDS for each species
#49
TomJKono
opened
4 years ago
0
Multiple Trees in File
#48
mmckibben
opened
4 years ago
6
Fetch XML ParseError
#47
mmckibben
closed
5 years ago
5
Dev
#46
TomJKono
closed
5 years ago
0
The logistic P value is only valid for the 41 genomes
#45
lilei1
opened
5 years ago
0
BAD_Mutations Incorrectly Back-translates from PASTA
#44
TomJKono
closed
7 years ago
1
Doesn't find HyPhy properly
#43
mojaveazure
opened
7 years ago
0
Add Logistic Regression to Prediction
#42
TomJKono
opened
7 years ago
0
Sanitize sequence names before alignment
#41
TomJKono
closed
7 years ago
1
Add Filtering of Species Databases
#40
TomJKono
opened
7 years ago
0
Fail nicely when "required" arguments are not specified
#39
TomJKono
opened
7 years ago
0
No output written to output dir with silent error
#38
kate-crosby
opened
7 years ago
3
makeblastdb
#37
kate-crosby
closed
7 years ago
1
Fail gracefully when no BLAST hits
#36
TomJKono
closed
8 years ago
1
Add command for dowloading in Mannual
#35
lilei1
closed
8 years ago
1
Off-by-one error in HyPhy script?
#34
TomJKono
closed
8 years ago
1
Skip sequences with ambiguous nucleotides
#33
TomJKono
closed
8 years ago
1
Compile HyPhy results
#32
TomJKono
closed
8 years ago
1
The fields in header of the prediction output file inconsistent with the ones with NOSNP
#31
lilei1
closed
8 years ago
1
Error in the path of the predict step!
#30
lilei1
closed
8 years ago
1
Warning: you may need to install requests if your python don't have this module
#29
lilei1
closed
8 years ago
1
Warnning: Install pasta need specific DendroPy-3.12.3
#28
lilei1
closed
8 years ago
1
run "setup" in MSI, HYPHY and PASTA can not set path automatically
#27
lilei1
opened
8 years ago
1
create new directories
#26
lilei1
closed
8 years ago
1
'Hordeum_vulgare' in below part shoud be 'hordeum_vulgare'
#25
lilei1
closed
8 years ago
1
Clarifying manual text
#24
pmorrell
closed
8 years ago
1
Missing Pasta
#23
Aerin13
opened
8 years ago
0
Inconsistant species naming
#22
Aerin13
opened
8 years ago
0
Sanitize Newick trees before copying into output directory
#21
TomJKono
closed
8 years ago
2
pasta dies
#20
fayjustin
closed
8 years ago
1
JGI Login Broken Again
#19
TomJKono
closed
8 years ago
2
empty temporary substitutions file
#18
fayjustin
closed
8 years ago
1
Target species not excluded
#17
fayjustin
closed
8 years ago
1
Bad fasta parse
#16
fayjustin
closed
8 years ago
1
HyPhy path in config file won't generate
#15
Aerin13
opened
8 years ago
1
Installing dependencies error
#14
ChaochihL
opened
8 years ago
0
Example setup code doesn't output usable config file
#13
Aerin13
opened
8 years ago
2
Add UMN MSI module instructions to User Manual
#12
TomJKono
closed
8 years ago
1
hyphy command not working
#11
fayjustin
closed
8 years ago
0
bad path
#10
fayjustin
closed
8 years ago
1
Missing sequence in fasta file
#9
fayjustin
closed
8 years ago
3
Safer shell options
#8
pmorrell
closed
9 years ago
0
Updated README.md text
#7
pmorrell
closed
9 years ago
1
BioPython check for fetch
#6
mojaveazure
opened
9 years ago
4
Check for required programs in $PATH
#5
TomJKono
closed
9 years ago
0
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