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Example use case creating an ``PairwiseAlignment`` instance as per the tutorial:
```pycon
>>> from Bio import Align
>>> aligner = Align.PairwiseAligner()
>>> seq1 = "GAACT"
>>> seq2 = "GAT"
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First issue was when I had to create multi-level/nested output directories on CLI as it won't automatically get generated by running the code. The rest are due to deprecated biopython modules hence th…
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**What should this tool do?**
This tool should count the number of differences or "point mutations" when two equal-length sequences are aligned and compared.
**Is there an existing reference imple…
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Hey,
I downloaded the most recent EFI 0.8.9 from your repo but noticed a substantial boot time difference from the 0.8.7 that I previously had. The old one just flies without ever stopping on any l…
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Hi,
This is great tool, i have used version 1. Now working with version2. I managed to install with conda, however i am getting following error
**wgd -h**
Usage: wgd [OPTIONS] COMMAND [ARGS]...
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I'm using pyhmmer to search a small number of profiles (for example custom profiles, not from Pfam) against large databases, such as UniProt. Here are a few things I have questions about:
1. Becaus…
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Hi,
After running the placement of metaG sequences of the nasA gene and labelled the placements, I tried to relabel eht epa-result.newick tree with the following command that seems correct:
```
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There are some problems with database lockups which seem to be caused by slow queries. I set `log_min_duration_statement=3000` and collecting any slow queries in this issue. These should be optimized,…