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chasewnelson
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SNPGenie
Program for estimating πN/πS, dN/dS, and other diversity measures from next-generation sequencing data
GNU General Public License v3.0
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problem with minfreq
#74
wantingwei
opened
6 months ago
5
Warning for coverage and nucleotide sums
#73
shamavirani
closed
8 months ago
3
Issue with SNPGenie_sliding_windows.R
#72
OmonkeyGOD
closed
1 year ago
4
No snps problems
#71
NiklausMikaelson12138
opened
1 year ago
4
VCF has no header
#70
NiklausMikaelson12138
opened
1 year ago
0
gtf2revcom.pl script issue
#69
georgysemenov
closed
1 year ago
2
Using SNPGenie on VCF from RAD-seq
#68
AudeCaizergues
opened
1 year ago
1
CDS annotation(s) does not have a gene_id
#67
frith6
closed
1 year ago
2
Need help to determine method for inference of convergent evolution
#66
qianxuans
opened
1 year ago
1
GTF file does not contain any sense (+) strand products
#65
dferran1
opened
1 year ago
12
How to join the output for a whole genome analysis
#64
pabloangulo7
opened
1 year ago
5
All classified as synonymous
#63
marotbone
closed
1 year ago
3
within-host diversity analysis : one individual, different time-points
#62
PegahDan
closed
1 year ago
4
within-host diversity influenza whole genome
#61
Su06690
closed
2 years ago
11
Coverage warning
#60
dinahparker
closed
2 years ago
4
SNP genie
#59
Ravy-LFL
opened
2 years ago
0
Empty output
#58
White-Shinobi
closed
2 years ago
8
What is the best option?
#57
glaudelrio
opened
2 years ago
1
Negative values for mean_gdiv_polymorphic
#56
peterdfields
opened
2 years ago
1
triplet error for spliced proteins
#55
hrrsjeong
opened
3 years ago
2
unsure how SNPgenie does the polarization of mutations
#54
mufernando
opened
3 years ago
1
Sliding window analysis for the spliced protein
#53
Chongli-90
closed
1 year ago
5
sliding_window script requires different headers than between_group output file generates
#52
passdan
opened
3 years ago
4
NONREF_NONPOLY and population_summary.txt empty
#51
nicolo-tellini
opened
3 years ago
2
pi cluster within-pool
#50
aspitaleri
opened
3 years ago
11
Question on interpreting the output parameters
#49
Chongli-90
closed
1 year ago
5
Question about calculating pi within a window
#48
deborahmleigh
opened
3 years ago
21
Watterson's theta and Tajima's D estimates
#47
sqiu86
closed
2 years ago
9
comments on dN/dS and pi
#46
aspitaleri
closed
3 years ago
1
gtf -strand convert to + strand
#45
zlc289
opened
3 years ago
2
analysing within-host diversity
#44
aspitaleri
opened
3 years ago
12
SNPGenie for bacterial samples from the same lineage
#43
arredondo23
closed
3 years ago
6
WARNING: AD must list numbers
#42
ireneIta
opened
3 years ago
6
mid-sequence STOP codon in the sequence
#41
jsan4christ
opened
3 years ago
1
SNPgenie for one bacterial strain
#40
SolayMane
opened
3 years ago
1
Advice on multi-sample, multi-species, multi-contig analyses for both πN/πS and dN/dS
#39
andreaswallberg
opened
4 years ago
4
specify genetic code?
#38
nathanerank
opened
4 years ago
3
snpgenie\_within\_group.pl: Question about input file formats
#37
annasimonsen
opened
4 years ago
2
error in running the SNPGenie
#36
shiyi-pan
opened
4 years ago
16
How to properly format VCF for snpgenie.pl (when using VCFs from multiple isolates of a population)
#35
maxgmarin
closed
4 years ago
7
between pops with vcf?
#34
karenbobier
closed
4 years ago
3
Making a vcf file by hand: ## WARNING: ## The SNP Report table_1.csv has no header.
#33
padpadpadpad
closed
4 years ago
3
Ignore genes that are not multiples of 3
#32
jckhearn
opened
4 years ago
2
Tag a release?
#31
druvus
closed
4 years ago
2
Fix shebang
#30
druvus
closed
4 years ago
0
reverse compliment
#29
harpur
closed
4 years ago
6
Understanding how within-between group works.
#28
migrau
closed
4 years ago
3
Missing sites in FASTA files
#27
sialsaffar
closed
4 years ago
3
Hello, I am trying to run snpgenie_wthin_group.pl after installing Parallel::ForkManager (with -force option) and get the error message: MacBookPro:SNPGenie-master julia$ perl snpgenie_within_group.pl --fasta_file_name=compl_cons_ORF --gtf_file_name=GGS.gtf Can't locate Parallel/ForkManager.pm in @INC (@INC contains: /Library/Perl/5.16/darwin-thread-multi-2level /Library/Perl/5.16 /Network/Library/Perl/5.16/darwin-thread-multi-2level /Network/Library/Perl/5.16 /Library/Perl/Updates/5.16.2/darwin-thread-multi-2level /Library/Perl/Updates/5.16.2 /System/Library/Perl/5.16/darwin-thread-multi-2level /System/Library/Perl/5.16 /System/Library/Perl/Extras/5.16/darwin-thread-multi-2level /System/Library/Perl/Extras/5.16 .) at snpgenie_within_group.pl line 62. BEGIN failed--compilation aborted at snpgenie_within_group.pl line 62. Do you have any idea what I can do to fix it? Thanks!!!
#26
jhillung
closed
4 years ago
3
Batch processing
#25
mhopken
closed
4 years ago
8
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