jaumlrc ProphET issues - Githubissues

jaumlrc / ProphET

10 stars 10 forks source link

issues

Newest

Newest Most commented Recently updated Oldest Least commented Least recently updated

gff_rewrite.pl stop in one place and don't move

#53 nienie123123 opened 1 year ago
0
Installation and running

#52 Songhaoqiu opened 2 years ago
0
INSTALL.pl script error "cat:...No such file or directory"

#51 rorycave opened 2 years ago
0
Running ProphET against multiple genomes

#50 JosephWestley opened 3 years ago
0
Regarding attL and attR identification in predicted prophage sequence

#49 shakti83kumar opened 3 years ago
0
GFF converter not working

#48 hayleyjaywilson opened 3 years ago
0
GFF compatibility (Prooka output --compliant flag)

#47 nilesh-tawari closed 3 years ago
1
Compatibility with Prokka generated GFF using (--compliant) option

#46 nilesh-tawari opened 3 years ago
3
GFF format convert trouble

#45 PaolaLis8 closed 3 years ago
0
Unable to find the transcript and gene associated to the CDS

#44 stefjanson closed 4 years ago
2
please provide a clean install

#43 phiweger opened 4 years ago
4
What tool(s) from EMBOSS do you need?

#42 tseemann opened 4 years ago
0
Missing description

#41 tseemann opened 4 years ago
0
Deprecated database when using ./INSTALL.pl or ./INSTALL.pl --update_db_only

#40 gkapatai opened 4 years ago
2
Update ProphET_standalone.pl to use RealBin

#39 microbioticajon opened 4 years ago
4
GFFFile module

#38 mariemh23 opened 5 years ago
3
Update ProphET_standalone.pl RealBin

#37 microbioticajon closed 2 years ago
0
Ideas for updating ProphET

#36 nickp60 opened 5 years ago
0
[WIP] Various Updates to ProphET

#35 nickp60 closed 5 years ago
0
Corrupt FASTA File during install

#34 Hana288 opened 5 years ago
3
blastall error

#33 yuq1993 opened 6 years ago
0
Issue near ORI

#32 gustavo11 opened 6 years ago
0
Consolidate input: both coding sequences and tRNA could only be provided as part of the same GFF file

#31 gustavo11 closed 6 years ago
0
Phage genome download from ncbi

#30 ovpop100 opened 6 years ago
5
Update only

#29 gustavo11 closed 6 years ago
0
Add to each phage db directory a file containing a summary of phage db stats

#28 gustavo11 closed 6 years ago
0
Consider maintaining a copy of all phage db that were used

#27 gustavo11 closed 6 years ago
0
Include in TravisCI a test for executions using tRNA as a separate file

#26 gustavo11 closed 6 years ago
1
Travis CI checks should be less stringent

#25 gustavo11 closed 6 years ago
1
Database updating

#24 kabilov closed 6 years ago
3
Some of the log files are being saved in the base directory of execution and later copied to output dir

#23 gustavo11 opened 6 years ago
0
Adapt application to blast+

#22 gustavo11 opened 6 years ago
0
Github release

#21 Takadonet closed 6 years ago
2
GFF format trouble

#20 mariemh23 opened 6 years ago
21
Could not find fetch_genomes_based_on_taxid.xml when running INSTALL.pl

#19 scottdaniel closed 6 years ago
1
There are two points in the code where STOP codons are discarded. Remove redundancy.

#18 gustavo11 closed 6 years ago
1
ABC transporters are not being removed from ProphET database

#17 gustavo11 closed 7 years ago
0
Setting up travis CI

#16 gustavo11 closed 7 years ago
0
obtain_prot_with_annot_seq.pl seems to be unnecessary

#15 gustavo11 opened 7 years ago
0
Translate to english comments

#14 gustavo11 closed 7 years ago
0
To provide a more extensive description of the prophages found

#13 gustavo11 closed 7 years ago
1
To provide a better description of the files generated

#12 gustavo11 closed 6 years ago
1
Investigate the possibility of taking output of Prokka

#11 gustavo11 opened 7 years ago
7
Error on line 119 of INSTALL.pl

#10 gustavo11 closed 7 years ago
0
The script is considering part of GFF description as sequence ids

#9 gustavo11 closed 7 years ago
0
Include in the manual the format of GFF that should be used and how to convert to that format

#8 gustavo11 closed 6 years ago
0
Generate file reporting the day of Prophage database update and stats about that database

#7 gustavo11 closed 6 years ago
0
Output GFFs reporting prophage gene coordinates and annotation

#6 gustavo11 opened 7 years ago
0
Improve graph depicting genes, genomes and predicted prophage

#5 gustavo11 opened 7 years ago
0
Assign name to predicted phages

#4 gustavo11 opened 7 years ago
0