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The pairwise alignment done in `rescue_mate` cuts out a much larger segment of the reference compared to when we can use seeds. This makes the pairwise alignment much slower for those instances (anecd…
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### Discussed in https://github.com/scikit-bio/scikit-bio/discussions/1973
@mortonjt @wasade Will appreciate your thoughts!
Originally posted by **qiyunzhu** March 17, 2024
Here I am descri…
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Good day,
I'm currently working on the assembly of a large mammalian genome. I would like to perform the reference-assisted scaffolding using ragout. However, I cannot run progressive cactus on the g…
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flake8 has built in code complexity checks using the flag `--max-complexity`. Running with max-complexity 10, we get (as an example)
```
skbio/alignment/_alignment.py:847:1: C901 'Alignment.subalignm…
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### Description
We basically want to port the seqan2 code to seqan3 that lets us compute an MSA.
Based on the structures in seqan2, this could be the structure for seqan3:
![MSA2](https://us…
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Hello,
when performing a virulign analysis and exporting it as a global alignment the following error pops up (repeatedly for every element of the alignment). It confuses me somehow.
Warning: Ne…
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A novel exact pairwise alignment algorithm, namely the wavefront alignment algorithm (WFA) has been proposed recently in September 2020 (big thanks to @dlaehnemann for noting this!):
[Marco-Sola, S…
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Hi skbio devs,
I'm seeing what I think of as odd behavior from the alignments.local_pairwise_align_ssw function. I've written a script which takes an unaligned, multisequence fasta file and uses this…
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Currently, snp-dists only cares about gaps in *pairwise* comparison. However, common alignment tools such as MEGA have a [complete deletion mode](https://www.megasoftware.net/web_help_7/rh_alignment_g…