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The complete PhyLiNC output for a simulated 10 taxon 1 reticulation 2000 MSA sites dataset, on the PhD laptop. I set the maximum number of reticulations it should try to 2, and turns out that PhyLiNC …
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Hi @jmcbroome,
Many thanks for developing autolin! I did noticed that autolin can be used with parsimony phylogenies, but I wonder if it can be used on approximately-maximum-likelihood phylogeneti…
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Create phylogeny for each sample.
- [x] Create representative reference set to use as a whole genome backbone
- [x] Same for ompa gene only
- [ ] Create bed file of recombination regions to mask …
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**Is your feature request related to a problem? Please describe.**
Parsl currently supports either pinning each worker to a single accelerator or no pinning at all. I want to pin each worker to more …
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Hi. I'm running MrBayes on macOS Mojave (ver. 10.14.6). Although the software looks working, the likelihood gets fixed at a specific value after a certain generations (printed screen attached). It dep…
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RNeXML should optionally be able to include all the basic metadata listed on the [MIAPA checklist](https://github.com/miapa/miapa/blob/master/checklist/MIAPA-checklist.md), hopefully guiding users tha…
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Hello,
We are attempting to assign peptides to either the mouse or human proteome. To do this, we were using the human, mouse, or both designation in the proteins.name column of the DIA-NN report.tsv…
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Detailed future work ideas, such that we can remove them from the supplement:
\section{Detailed Future Work Ideas}
\subsection{Runtime Improvements}
\subsubsection{Improve virtual re-rooting du…
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@JamesBarbetti I think something untoward is happening in the parsimony code.
Using exactly the same data and commandline, I get very different outputs from the code compiled on 27 Apr versus 15 Ma…
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- fidelity
- process fidelity
- purity
- diamond norm
- others?