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We can start with the most poplar aminoacid substitution matrices (like PAM250) and adding a switch in command line arguments.
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Hi, I installed Phylophlan from conda in new enviroment and ran the following command:
`phylophlan -i metawrap_70_10_bins/ -d amphora2 --diversity medium -f ~/phylophlan/supertree_nt.cfg --output_fol…
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I am interested in calling all the mismatches/conversions in my RNA modification dataset that is generated using Illumina TruSeq protocol (dUTP). I am using the JACUSA2 pileup method for this step. Si…
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This issue is inspired by [this](https://math.stackexchange.com/questions/4250154/cayley-hamilton-in-macaulay2) Stack Exchange question that I randomly ran into.
Would be great if the following wor…
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This object should should contain a numpy `array` that holds the substitution values and support `__getitem__`. Ideally, it leverages numpy as much as possible through `array` lookups instead of `dict…
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#### System info
```python
import sys; print(sys.version)
import platform; print(platform.python_implementation()); print(platform.platform())
import Bio; print(Bio.__version__)
```
```
3.8.19…
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The following has been deprecated from the BioPython repo
`from Bio.SubsMat.MatrixInfo import blosum62`
One way to fix it is to replace with
```
# from Bio.SubsMat.MatrixInfo import blosum62
from…
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[Class `ProteinEmbedding`](https://github.com/scikit-bio/scikit-bio/blob/545c9859635a5b8514bd9fd599475717c533f108/skbio/embedding/_protein.py#L29-L121) implements a data structure for the storage of p…
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We should provide backward and forward substitution algorithms for sparse matrices.
See: https://github.com/mikera/vectorz/issues/29 for motivation
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Hi,
I've been trying to resolve this deprecation by using the Bio.Align.PairwiseAligner module but have not been able to do so.
We use a python function to determine the alignment score in order t…