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I am parsing my sequences with SeqIO and I have ambiguous DNA specified in my alphabet. I successfully translate the sequence and store in a list called "protein". When I build the alignment however:
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## Expected Behavior
easy-search should finish execution without errors
## Current Behavior
Error during pre-filter step
> Index table k-mer threshold: 0 at k-mer size 15
> Index table: …
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I see the [BMGE](https://link.springer.com/article/10.1186/1471-2148-10-210) tool is already in the Galaxy ToolShed (https://testtoolshed.g2.bx.psu.edu/view/dcorreia/bmge/a943abb980db), but not yet on…
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I would like to calculate the dN and dS between two sequences, to do so I had to make a codon alignment such like that:
(*Peter: I adjusted the formatting and added the missing import lines*)
`…
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After discussion with @InaMBerry, some of the below might be possible:
- Marking Primer-induced errors
- This would require parsing the trim_stats files in order to know how much of the primer was a…
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This is a great tool for visualsing nucleotide changes, thanks for making it available to the community!
A related use case would be to visualise amino acid changes vs a reference (eg if giving sni…
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Hi, I'm trying to use read2tree, but after it finishes making the orthologous genes selection and allignment it gives me the error I'm attaching. I suspect that it has something to do with this speci…
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This is unsupported (print 30 times the character `=`)
```python
print(f"{'':=
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I wasn't able to test #1333 (which adds support for parsing complex CDSs using GenBank files) because I didn't have translated (AA) fasta files around. This made me wonder why we need the AA sequences…
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`Bio.codonalign` was added to Biopython about 8 years ago. Currently this module is still considered to be experimental, and prints a `BiopythonExperimentalWarning` when imported:
```python
>>> fr…