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Hi,
I have two questions.
1. Can I run my own data using "test=true" option?
When I run the test data, it seems to work smoothly. But when I am running my own data with "perl METABOLIC-C.pl -t 40…
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Attached find some relevant log files and the run script
[mergelog.txt](https://github.com/jtamames/SqueezeMeta/files/7390210/mergelog.txt)
[syslog.txt](https://github.com/jtamames/SqueezeMeta/fil…
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Hi,
We have noticed a lack of consistency between Nextclade versions on at least one mutation:
The deletion of nucleotides 22029-22034 on previous versions (tested on 0.12.0 and 0.14.4) is trans…
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If so, how problematic are (1) large accessory genomes (ie each genome only contains a small subset of the species' gene pool, eg Prochlorococcus) and (2) high rates of recombination (eg Pneumococcus)…
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## Short description of the problem
I have followed the tutorial at https://merenlab.org/2016/11/08/pangenomics-v2/
Using anvi-pan-genome I have created PAN-GENOME.db of 143 complete genomes.
Now…
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**Versions**
Poppunk version 2.4.0
pp-sketchlib version 1.7.1
scikit-learn verson 0.24.2
python version 3.9.4
**Command used and output returned**
```
poppunk --create-db --output neiss…
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Hi John,
I've got a yet another minor bug to report here:
**Versions**
I am using PopPUNK v2.3.0 with pp-sketchlib 1.6.2, as provided by a conda environment built with
```sh
conda create -n pop…
flass updated
3 years ago
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Hi,
I was able to run Evolinc with the test data but now I am getting an error when using it on braker genome annotations. This is the error message
```
Tue Mar 9 17:39:39 UTC 2021
No fasta index…
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Hi all,
I want to create a graph combing the phylogenetic tree, fasta sequence, and some phenotypic traits.
When I first tried msaplot() to align the fasta sequence with the tree., there is no iss…
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Is it possible to get an accessory gene alignment or accessory gene file out of Panaroo?
Thanks