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I've read the paper for kmer-db and I weren't able to find anywhere whether kmer-db uses a seed for minhashing during the build step. I've ran kmer-db build twice (from KMC-counted kmers) and it seems…
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Dear authors, I am trying to reproduce the results in your publication and I was wondering if you can you please provide the structures and the corresponding code to reproduce the generation of the ma…
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Hello,
I read about issues about passing customized distance function to the UMAP. I realized that we can easily feed the UMAP with the distance matrix instead (#348 ). Right? So, for instance:
m…
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Possible synthetic task for comparison is evolving graphs to match target graphs by some distance metric, like edit distance of adjacency matrix. In DEAP/pymoo this can be implemented as evolution of …
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In MultitaskScaffoldSplitter, with certain datasets, you often see warning messages saying "two scaffolds match exactly?!?". This happens when the minimum Tanimoto distance between pairs of compounds …
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Joe at Uni Bristol looked into ways of improving distance storage and calculations. I past here some text.
**Problem**: I have sets of global climate data at a reasonably high spatial resolution (720…
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Hello, I have just installed conan on a linux-breathing machine and ran the test.py script from the terminal.
It found gromacs, mencoder and gnuplot OK (after I installed them) but seems not to find …
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Dear Ryan,
thanks for developing Bacsort. I'm trying to run it on a bunch of genomes from isolates and cluster_genera.py fails every time, but I can't interpret the error. Do you have any ideas or di…
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Would be via [`get_all_neighbors(...)`](https://pymatgen.org/pymatgen.core.structure.html?highlight=structure#pymatgen.core.structure.IStructure.get_all_neighbors) or probably preferably [`get_si…
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For example, we could look for associations between the geographic distribution of viruses and phylogeny. This could be done by computing euclidean distances between where (geographically) a particula…