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[One of our spack environments](https://github.com/FairRootGroup/FairSoft/blob/7ebe61adcb0ddbf65cba21e1c93fce5728a2fbbb/test/env/fairlogger.yaml) that has worked with spack `0.14` no longer works with…
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As noted in a comment to #56, the substitution score from and to the Z dummy block is always 0. This is used in `PBclust` to build the distance matrix, and to compare sequences with the `--compare` op…
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Hello!
I am trying to understand how exactly are bit scores and E-values calculated. I found the formula in [The Statistics of Sequence Similarity Scores](https://www.ncbi.nlm.nih.gov/BLAST/tutorial…
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I get the following error when I run the tutorial. What am I doing wrong?
```
$ python GIANA4.1.py -f data/tutorial.txt
Traceback (most recent call last):
File "/home/trevizani/prog/GIANA/GIANA4…
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Right now in `linalg.py`, I'm using `numpy.linalg.inv()` for matrix inverses.
I'd like to implement it from scratch instead, but it looks rather difficult...
[Cholesky decomposition](https://en.wi…
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Hello,
I'm currently working on a tool that calls pairwise distances between large numbers of SARS-CoV-2 genome sequences. One of the issues with this kind of bioinformatics is that these sequences…
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> Hello,
> I was wondering whether it is among your plans (and whether it is possible to implement) to add protein mixture models to RaxML, particularly C10-C60 (http://bioinformatics.oxfordjournals.o…
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Noticed on some recent CI builds, e.g Python 3.7 with setuptools-65.2.0 wheel-0.37.1 (which was failing for a different issue) https://github.com/biopython/biopython/runs/7970592569?check_suite_focus=…
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This is more a question about existing features than a new feature request; if these features are not already native to BEAST, then I imagine they'll have to be implemented in a plugin.
I'm using B…
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I have two nucleotide sequences: The query is an ORF, the target is a truncated genome sequence, containing an homologous ORF with a high identity to the query.
Despite the high similarity, `mmseqs…