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I am wondering how can i add something like [Pseudomonas aeruginosa ](https://en.wikipedia.org/wiki/Pseudomonas_aeruginosa#:~:text=Pseudomonas%20aeruginosa%20is%20a%20common,of%20considerable%20medica…
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Right now there are 155 database cross-references in UniProt:
- http://www.uniprot.org/database/
I want to discuss here
- [ ] which ones are essential
- [ ] a reasonable, flexible model for cross-ref…
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Suggestions provided by @haruosuz
- bactopia can accept GFF3 files (.gff) instead of FASTA files (.fna) as input, like PIRATE and Roary, to skip Prokka?
- bactopia can do alignment trimming (e.g. …
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I tried running your Prophage_Tracer for the first time today and I got this error
awk: cmd. line:1: fatal: division by zero attempted
I followed your directions to index with bwa, then map with b…
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```
What steps will reproduce the problem?
1. Open AltAnalyze and begin
2. Click on Add New Species
3. receive error and program crashes
What is the expected output? What do you see instead?
Wha…
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Hi there,
I have a couple of questions...
1) I am running SwiftOrtho on around 700 bacterial genomes. I substituted step 1 with a diamond run (with a suitably increased max-hits pram) and by run…
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Dear PhenotypeSeeker Development Team,
I hope this message finds you well. I am writing to report an issue I encountered while using PhenotypeSeeker software. During the model generation phase (std…
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Hey, I am engaged in the analysis of bacterial genomes. Since bacteria do not have introns, bacterial genomes are simpler compared to eukaryotes. Therefore, can software be applied to bacteria? Or can…
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- last version of the raw reads for Leptospira assemblies **did not have quality check** nor **trimming** done before assembly.
- to assure the quality of all isolates before assemblies, we will **re…
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Hi Nick,
I'm using Gubbins v3.3.5 as indicated below:
```
run_gubbins.py $PREFIX-CLEAN_NoRef.aln --first-tree-builder iqtree \
--tree-builder iqtree \
--tree-args " -T…