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What is the default for the --min_num_markers parameter? The wiki says it's 100 & 34 respectively for the phylophlan and amphora2 marker sets respectively, however `phylophlan -h` shows that it's set …
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Add explaination on how to do the polynomial approximation of 1/x
It mightbe cool to have the polynomial approximatoin used for ridge regression. Can we do it?
https://github.com/Scinawa/quantumalg…
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I'm finding it difficult to get hits for short sequences (around 10 aminoacids in length). I've already raised the evalue cutoff (-e) which helped in including more hits. However I'm still not getting…
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The interpolation coordinate is off by one in 'wrap' mode.
Test case:
a = array([0, 1, 0, -1.])
x = linspace(0, 8, 8, endpoint=False)
y = map_coordinate(a, [x], mode='wrap')
ynp = numpy.take(a, int64…
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Over the past weekend, I did some soul searching on where I stand between F# and Hack, which lead me into a deep-dive that anyone interested can read here: https://arendjr.nl/2021/09/js-pipe-proposal-…
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This module needs example use cases and documentation.
I can't figure out how to use it.
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Thanks for the great looking tool. My question/issue relates to phylophlan metagenomic: Is there a simple way to download, extract, and point to the database manually?
Have spent the last day tryin…
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Hey,
I am using `amici 0.11.1` in the develop version on a WSL.
I created an SBML model using COPASI. After exporting and importing the SBML file into a new COPASI session, I was able to successfu…
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Notes from @elambrinaki on Slack:
> Overall, I would love to discuss an approach for testing whether a standard collection existed and how it changed.
> Assume the standard order of stories IDs in…
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Dear Phylophlan Team:
i was downloaded protein file form NCBI and change the suffix to '.faa', files includes "Candidatus Methanomethylophilus alvus Mx1201"(https://www.ncbi.nlm.nih.gov/nucco…