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SionBayliss
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PIRATE
A toolbox for pangenome analysis and threshold evaluation.
GNU General Public License v3.0
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understanding pirate results
#88
happymanmohit
opened
1 month ago
0
PIRATE.pangenome_summary.txt
#87
haruosuz
opened
4 months ago
6
stuck at threshold 60 during MCL clustering
#86
jiyanxu
closed
9 months ago
3
Running on large dataset
#85
NicolasNaepflin
closed
1 year ago
2
Missing output files and coregenom files
#84
mrojas80
closed
1 year ago
3
Bump version in new release
#83
rpetit3
closed
2 years ago
4
problem in installation
#82
ariasamin
closed
2 years ago
9
For some single loci, a gene family but for others not.
#81
margotmdr
closed
2 years ago
1
Error when running PIRATE MCL process
#80
whositwhatnow
closed
2 years ago
0
Undefined subroutine &main::translate called
#79
salrodpal
closed
2 years ago
2
- ERROR: link_clusters.pl failed.
#78
fengyuchengdu
closed
2 years ago
1
Average_dose =1 is appropriate to determine whether a gene family is a single copy？
#77
junhiuqiu
closed
2 years ago
1
Feature request: Option to include original IDs and annotations in fasta headers for align_features_sequences script
#76
alexweisberg
closed
2 years ago
2
How do you tell which gene families are single-copy or multi-copy?
#75
junhiuqiu
closed
2 years ago
2
Error after MCL clustering step
#74
alexweisberg
closed
2 years ago
5
PIRATE_plots.pdf created by plot_summary.R
#73
haruosuz
closed
2 years ago
1
Fix bug when number of GFFs is large
#72
dorbarker
closed
2 years ago
1
Output gene sequences to run gene alignment separately
#71
boasvdp
closed
2 years ago
4
Missing genome in output
#70
iferres
closed
2 years ago
12
error observed during "aligning all feature sequences"
#69
fengyuchengdu
closed
3 years ago
2
extract_feature_sequences.pl failed
#68
3josh4
closed
3 years ago
2
Confused with terminology/output
#67
FilipeMatteoli
closed
3 years ago
1
Output Files
#66
JChristopherEllis
closed
3 years ago
3
gaps in core_alignment.fasta
#65
haruosuz
closed
3 years ago
1
mafft alignment number of threads
#64
luciagrami
closed
3 years ago
1
README.md options
#63
haruosuz
opened
3 years ago
7
0 core loci
#62
haruosuz
closed
3 years ago
3
Error in core genome alignment
#61
furqan915
closed
3 years ago
5
is it possible to adjust the core gene threshold?
#60
ramiroricardo
opened
3 years ago
5
why and how PIRATE create pangenome.gfa file?
#59
limin321
closed
3 years ago
1
blastp failes
#58
jolindadekorne
closed
3 years ago
7
Minor fix on line 305
#57
kant
closed
3 years ago
1
Question about core genome concatenation
#56
rx32940
closed
3 years ago
3
Revert "Add minimum feature length option"
#55
SionBayliss
closed
3 years ago
0
conda installation issue
#54
furqan915
closed
3 years ago
1
Add minimum feature length option
#53
rpetit3
closed
3 years ago
1
Use with eukaryotic/intron containing models
#52
hyphaltip
closed
3 years ago
3
Min length of gene families
#51
plasmid02
closed
3 years ago
8
need suggestions on my PIRATE commend.
#50
limin321
closed
3 years ago
11
Plasmid comparison
#49
jellila
closed
3 years ago
3
PIRATE create unexpected output when using -f "tRNA,rRNA"
#48
limin321
closed
3 years ago
1
gene_families and pangenome gff file do not match
#47
maguileraf
closed
3 years ago
3
PIRATE to Roary
#46
JParraV
closed
3 years ago
2
questions on output files
#45
limin321
closed
3 years ago
4
- creating co-ordinate files Failed
#44
limin321
closed
3 years ago
9
Pan genome from genomes of contigs
#43
milnus
closed
3 years ago
3
Annotations did not match contig names
#42
Noahw15
closed
4 years ago
3
Representative pan genes FASTA ?
#41
tseemann
closed
4 years ago
3
Missing --version flag
#40
tseemann
closed
4 years ago
2
PIRATE -c doesn't work (but --check does)
#39
tseemann
closed
4 years ago
1
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