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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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Some ideas from a chat with Fred Jaya. Use the wiki to give a few examples of simple benchmarks, e.g.
1. RaxML vs. IQ-TREE on individual loci (fix models to be equal, assess trees in one piece of s…
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Thank you guys for throwing in the documentation. Segregating this from the other Issue.
Is there any possibility to include more of the k-diffusion samplers? https://github.com/crowsonkb/k-diffusi…
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These three annotation types are related as they build on each other to make statements of higher-order reach and complexity. Here, more fundamental annotations are/can be used as input or evidence i…
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Dear Developers,
Thank you for your work. I tried TedSim and manage to simulate a dataset as explained in the vignette.
## Context
The default implementation of TedSim allows for simulation o…
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Hello,
We recently used TreeTime to infer ancestral sequences for a set of Influenza samples and then visualized the phylogenetic tree with the branches being annotated by the inferred mutations.
…
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Several commands describe themselves in their module docstring, which they provide to the argparse parser as their description. However, the argparse formatter configuration mangles these descriptions…
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Hey all-- I'm opening up an issue for us to start bashing away at an outline for the second paper. a particular goal is to have a solid list of the analyses we want to do and then later, delegation of…
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I took a look at https://github.com/vgteam/sequenceTubeMap but it appears it's not possible to just look at the graph itself - it only let's us visualize aligned reads.
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It's hard to believe when we talked about this before I didn't realize how easy it would be, but I wrote a function to add new sequences (i.e. inferred intermediates from a phylo program) to an existi…