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### Setup
I am reporting a problem with :
3.8.12 (default, Oct 12 2021, 03:01:40) [MSC v.1916 64 bit (AMD64)]
CPython
Windows-10-10.0.17134-SP0
1.78
### Expected behaviour
I encountered u…
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Although very useful in its current form, as far as I can tell,`Bio.Phylo.PAML` does not currently extract positively selected sites from the codeml output file when parsing them. In light of PAML's t…
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As discussed in a [stack overflow thread](https://stackoverflow.com/questions/44320675/differences-between-biopython-ncbi-entrez-esummary-output-and-r-package-output/45952296?noredirect=1#comment79192…
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In an environment without some of the paths listed in the config, e.g. `/work/software` directory, `engine run` will throw an error that should probably be caught and handled. E.g.,
```
(barrelseq)…
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Hi Matt,
A girl in my lab is trying to set up ITEP with some bacterial genomes. She ran into an issue: convertGenbank2table.py fails because some of here genbank files (downloaded from RAST) have join…
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Dear Sir or Madam:
I have got the following error messages:
```
Encountered problems while solving:
- nothing provides requested kraken 2.0**
```
```
rsync_from_ncbi.pl: unexpected FTP path…
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This is supported in clotho.submit, but not run. I don't think it makes sense.. it's certainly not intuitive.
i.e. calling `clotho.run` from browser API and passing: `{id: "module.function", args : […
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Thanks for the great tool and your help both on and offline.
I'm curious about the decision to `fix_fasta_header` before processing the FASTA. This makes it basically impossible (as far as I can t…
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Since #474 we have a Test Class that all coordinates formats should share for testing.
This issue is here to track progress about it
- [ ] test_coordinates.py
- [x] test_dcd.py
- [ ] test_dlpoly…
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Dear Ian,
I have detected a couple of inconsistencies when using the Chloe web portal. Specifically, when I upload the chloroplast genome of
[Arabidopsis thaliana](https://github.com/ian-small/ch…