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Congratulations! The datamonkey family increased.
I need help to understand the job 66f6dd49de2c0658dec4fe5d because:
1. The submitted file had 91 cds but ntax=80;
2. The alignment has 280 "codon…
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Thank you for your work.
When I run vadr 1.6.3 on this virus: https://www.ncbi.nlm.nih.gov/nuccore/KY933089 (fasta file)
I obtain nothing in the 'pass' tsv file.
In the 'fail' tsv file, I get t…
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For some reason there was an IndexError when running the method below, but since the variable `codon_alignment` was never initialized there was a UnboundLocalError raised as well claiming: _local vari…
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## Expected Behavior
Hello, when I run mmseq_gpu on my own data set, this error is reported. Is there any command restriction to prevent it from reporting such an error?
## Context
stdout:
sear…
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The filename is unclear but ``Doc/doc.rst`` and ``Doc/doc.tex`` are from @zruan for the codon alignment module. I assume one is generated from the other?
Perhaps this should be turned into a Tutori…
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This is a feature request/enhancement (tangentially related to issue #60).
I was wondering if there are plans to incorporate --junc-bed and --junc-bonus parameters in Miniprot, similar to the curre…
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When an alignment has a stop codon followed by gaps is detected as an early stop codon.
example:
```
>1
ACGTCA---TAG
>2
AC----TAA---
```
The `TAA` stop codon in the second sequence is a term…
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Hi! I'm a Master's Student using Aliview and DataMonkey to do my thesis, but I keep running into the same issue when I input my data into DataMonkey. Based on a set of instructions from a PhD student,…
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Here are three analyses, quite simple, each is a 3 partition analysis on a small COI alignment. The only difference between the three is the option for how to treat the branch lengths among partitions…
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The attached files misalign a bit. If you run virulign using the [nef](https://github.com/rega-cev/virulign/files/6044405/11676_nef.xml.gz) xml on [this alignment](https://github.com/rega-cev/virulig…