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180 Open 219 Closed
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Issues list

How can I have a clear visualization of Roary results by using roary_plots.py if I have more than 500 genomes?
#626 opened Nov 3, 2024 by lingyuyuyuyu
KeyError issue when running roary_plots.py on nwk
#624 opened Aug 19, 2024 by aryehjc
CDS ID tag incompatibility - 'ID=CDS:ENSB:O-Ndl8aNBRf4G1w' needs to be 'ID=ENSB_O-Ndl8aNBRf4G1w'
#623 opened Aug 9, 2024 by NickJD
MSG: Got a sequence without letters. Could not guess alphabet
#622 opened Jul 29, 2024 by hallkyl6
1
Cloud not obtain clear phylogenic tree
#621 opened Jun 26, 2024 by Ronykumawat
1
The number of pan-genes in gene_presence_absence.csv is less than each genome
#620 opened May 14, 2024 by Amilycd
How are genes with frameshift mutations/INDELS handled?
#619 opened Apr 29, 2024 by sydelstan
Use of uninitialized value in require at /usr/lib/x86_64-linux-gnu/perl5/5.34/Encode.pm line 70.
#618 opened Apr 18, 2024 by charlesshirima
Order of genes in alignment
#617 opened Apr 7, 2024 by BlabOaklandU
Roary grouping genes that don't meet similarity threshold (using -i 100, and -s)
#616 opened Mar 19, 2024 by LijMeh
6
How can I discover the genetic sequences that are used to group groups in roary?
#615 opened Mar 5, 2024 by Deblusantos
Issue with "Error: Cant access the groups file: clustered_proteins"
#614 opened Mar 2, 2024 by wayne1215
1
The singularity image pulled from docker://sangerpathogens/roary does not accept input gff files
#613 opened Feb 19, 2024 by dawnmy
2
cann't install roary 3.13 with mamba/conda
#612 opened Feb 19, 2024 by dawnmy
1
core_alignment.aln has lower and uppercase in sequences
#611 opened Feb 8, 2024 by samuelmontgomery
i cant install Roary by mamba
#610 opened Jan 24, 2024 by leech1225
3
roary_plots.py heatmap coregenome matrix empty
#609 opened Jan 18, 2024 by yjjj2002
Cant open file: 14L9VpZJtx/DNA16.gff.proteome.faa Please, help with this issue
#608 opened Jan 5, 2024 by alanxelena
Missing proteome.faa files
#607 opened Jan 2, 2024 by sydelstan
No newick file
#606 opened Nov 28, 2023 by Dabiguina94
2
how can i solve this issue
#605 opened Nov 12, 2023 by ryujinyuna
Number of conserved genes increases through genomoes
#604 opened Oct 31, 2023 by PauObregon
Strange Ouput
#603 opened Sep 29, 2023 by ShuyiF
2
number of conserved/unique genes.Rtab
#602 opened Sep 19, 2023 by kimTina321
EXCEPTION: Bio::Root::Exception ------------- MSG: Failed validation of sequence '1'. Invalid characters were: ''''''''''
#601 opened Sep 2, 2023 by Psedhai
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