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Hi All!
I would like to know how the phylogenetic tree is built. The only information provided is that the presence and absence of genes is used.
So .. the phylogenetic tree is built by aligning t…
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When using --db-type unordered when the CDS in the input are not ordered, we have an error :
```bash
2023-12-12 11:58:23 | INFO | Post-treatment of the data
Traceback (most recent call last…
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Describe the bug
No All_gene_collections_transcript_coverage.txt file is generated using metatranscriptome reads (metaT)
To Reproduce, see error:
Error:
[2022-03-29 23:40:53] Drawing element cyc…
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```
6 input contigs, 6 larger than 500 bp, N50 is 427,039 bp
Checking duplication of 6 contigs
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scaffold_73 appears duplicated: 100% identity over 10…
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Would be useful to take the core genome phylogeny and annotate the edges with _M. bovis_ genes that are considered virulent for for the species.
Step 1) BLAST the pangenome_reference file against…
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Hi there,
Thank you again for helping me the other day with the issues I was having. I've been able to run bambu successfully on some of my samples, and I have a couple of follow-up questions (I ho…
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- [x] There seems to be a lot of indentation issues (mixed tab/spaces?) in the ReadsAPI.spec file- it made things difficult to read. That should be fixed.
- [x] To future proof this, we need to have …
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# **This issue post is for prosperity and has already been reported.**
I have been using Panaroo for a while now but I am currently trying to take the DNA/Protein sequences reported in the combin…
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Hello,
I performed PIRATE on 205 bacterial genomes. I want to visualize the accessory genome network. Can you guide me on what to do next to generate files that can be visulized in graphia?
Thanks…
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Hi,
Thanks for this great program.
I'm having an issue when running diefense-finder on a large number of genomes and using the `unordered` db-type (for my purposes I require this instead of `gem…