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I think we need to centralize efforts on variable length sequences in pylearn2 and really get our act together. I know a lot of people (@bartvm @vdumoulin @laurent-dinh @pascanur) have thought about t…
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I'm running "IQ-TREE multicore version 2.3.6 for Linux x86 64-bit built Aug 1 2024" with the following command:
`/software/iqtree-v2.3.6/bin/iqtree2 -s test_aa.fa -m MIX+MF --prefix test`
followi…
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It would be handy if we could parse distance matrices from text files where only the lower/upper triangle is stored.
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A fairly simple example can cause a crash from CSE.
```
In [4]: x = Matrix(MatrixSymbol('x',2,1))
...: K = MatrixSymbol('K',2,1)
...: cse(x+K)
...:
```
I have attached the error bel…
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I've looked through the code and help pages, but I can't find a simple way to be able to simulate the means and covariances of the LNA over time - the simulation just returns draws from the LNA (at le…
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We currently use `pinv`, should probably use https://pytorch.org/docs/stable/generated/torch.linalg.lstsq.html instead (or maybe some third thing). Doesn't seem like a big issue so far though
ejnnr updated
4 months ago
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The following code worked in 1.10.1 but not in 1.11.1.
```python
from sympy import *
m1 = MatrixSymbol("m1", 2, 2)
m2 = MatrixSymbol("m2", 2, 2)
m3 = MatrixSymbol("m3", 2, 2)
Add(0, m1) # …
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Hi, thanks for this wonderful library!
I'm just wondering that since we have utilities like `read_fasta_file_as_list_of_pairs`, and also `run_all_scores` which runs a comprehensive evaluation, we c…
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The alignments are defined in such a way that it is not possible to have consecutive gaps. Here's a test case (to go in NeedlemanWunschTest. Requires 4bc1d20.):
``` java
@Test
public void testSin…
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Hi,
I have downloaded Phylophlan version 3.0.60 via conda and following example 1 (S.aureus) tutorial on github.
This is the command I am using:
` phylophlan -i input_genomes -d phylophlan --d…