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The species tree generated is correct, and the two species I'm interested in comparing are at a defined node of the tree (N2). For downstream analysis of orthologs between the two species, should I re…
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The list has the pombe genes that are missing human orthologs and the pombe gene paralogs that look OK to help out. There are about 23 genes that need checking/fixing.
- [x] [genes_with_odd_paralo…
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Hi,
I used panaroo to generate a lot of pangenomes. Now I want to segregate the "core" genes into a separate file. The summary file gives me the number of genes segregated into core or accessary geno…
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I ran panaroo with the mafft aligner for core genes and noticed a discrepancy in the number of core genes output by the summary_statistics.txt file vs the number of genes aligned in the aligned_gene_s…
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Dear Mr. Tang,
Thanks for developing this useful package. I have two questions when I plot the microsynteny visualization. The synteny line is very weaker in my figure, which is probably caused by …
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1. Should "Style" attribute be renamed to "Type"?
2. New element types:
- Complex (physically interacting sets of molecules that function as a coherent entity)
- Paralogs (entities that share com…
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based on the malacards mapping file
https://curation.pombase.org/dumps/latest_build/pombe-embl/external_data/disease/
malacards_data_for_chado_mondo_ids.tsv:hyperinsulinemic hypoglycemia, familial…
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Dear developer,
I tried to identify core loci of plasmids belonging to IncP-1 groups (ACCESSION: `BN000925 U67194 AB231906 AM157767 GQ983559 AM261282 AY950444 KC170283 KP324830 KX377410`)
Runn…
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Hi,
I am using Roary 3.12 on ~20,000 GFF files with 12 threads and 900GB of RAM. "roary" has been running for 9 days. I was wondering if there is any way or setting I can use to improve the running…
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I would like to have some external assessment of my smudgeplot. I have used following commands to generate it (as suggested on Smudgeplot README)
```
ls *.fq.gz > FILES
kmc -k21 -t4 -m25 -ci1 -…
ms-gx updated
3 years ago