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As I've been working on #549 to add support for SARS-CoV-2 references, I've had some trouble with running out of memory. I think it's partly that I'm running on equipment with less memory than I usual…
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While trying to write a test for issue #299, I discovered strange behaviour in the Gotoh alignment algorithm that we're using. Here's a small script to reproduce the problem:
```
import gotoh
gap_op…
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There are other algorithms that are available in TextDistance that may be considered.
### Edit based
- MLIPNS http://www.sial.iias.spb.su/files/386-386-1-PB.pdf
- Strcmp95 http://cpansearch.perl.…
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Hi there,
first of, this is an excellent library. I am utilizing it for a research project and had no issues installing and running it on Kaggle. Recently, however, Kaggle apparently upgraded to Py…
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Hi Jeff,
Thank you for the development of Parasail. It is an outstanding piece of software.
It seems that Parasail is not applying a gap extend penalty when we open gaps in the sequence.
My wo…
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The running time of Linculst in the threshold between 50% to 90% is normally the same. But why does Linclust‘s running time in the threshold 90% to 100% range gradually increase? The run time at 100% …
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Dear @ogotoh,
I have mapped protein sequences to a genome and observe in the alignment output (O1) that many codons that I expect to encode "S" or Serine are written as "J", which as far as I know …
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In the 09-Dec-2016.M01841 run, sample PNL4-3-1-V3LOOP_S73 reported a strange consensus sequence.
After digging into the problem, we found that a six-base insertion wasn't aligned with the codon bou…
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https://github.com/cfe-lab/MiCall/blob/f79fca0d135dd08d22c4324f9e81bc819db813ce/micall/utils/probe_finder.py#L127
I traced a bug to this function where if the input argument `seq` contains too many…
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The function in clustering is originally taken from and builds on lingpy's infomap-clustering (you might want to mention this in the function description), and it has some code that you never use:
…