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CDS_coordinates, by chromosome - ftp://ftp.ebi.ac.uk/pub/databases/pombase/pombe/CDS_Coordinates/
exon coordinates - ftp://ftp.pombase.org/pombe/Exon_Coordinates/
see https://github.com/pombase/…
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Hello,
I was testing Prokka and Roary for my genomes.
I followed the Prokka command for genome annotations but all .gff files of different samples have the identical .gff file names! Is this normal?…
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Hi,
I read your paper with great interest. Thanks for developing this tool. I also noticed some differences in methodology which perhaps you can help me understand further.
In the original ortho…
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Hello,
I used orthofinder to cluster orthologous groups from the proteomes of 7 plants and it worked great! I plan to infer gene trees for ~6000 of these OGs. I used trees_for_orthogroups.py to gene…
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Hi Dr. Soranzo,
Could you please provide some suggestions on how to how to identity 1:1 orthologs after the running of hcluster_sg_parser? What I was doing is import the output files into excel and…
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>This table is useful, but please comment on how gene function was inferred from sequence. Is this from GO terms based on closest known homolog? Is this manual or semi-automated curation? Additionally…
kubu4 updated
7 years ago
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I have a group of genes (appx 30) that I would like to check in different bacterial strains for positive selection using the abs-REL method. There are 2 issues that make me wonder whether I could draw…
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Hi Andrew,
I'm running Roary on three genomes, which I annotated with Prokka. Apparently the BLAST steps fails, although the program still finishes. The combined genes from the three genomes end up…
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Hi,
I have some quick questions about paralog splitting in roary:
- When running roary with split paralogs enabled (default option), I noticed that not all gene groups with paralogs get split. Thi…
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I tested this function you suggested in issue #282 but it's still confusing:
1) I used roary without using -s and results were as follows:
> Core genes (99%