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We currently report mutations relative to the reference sequences and relative to the nearest node in the reference tree, called private mutations. The former are derived straight from the alignment, …
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In order to perform the comparison analysis which identifies the care gap we need an estimation of effected population over time. More specifically, we want to know the projected number of active case…
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Hi,
I am running treetime with `treetime --covariation --confidence --clock-filter 5 --tree --aln --dates ' ` on a selection of N1 subtype influenza viruses and it is returning the following:
…
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Hello,
Do you consider adding binary alignement / models ?
Thanks,
Adrien
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# 🐛 Bug Report
We noticed that, for some reason, JSURL "'" converted to "%27" in the address bar of Chrome (Windows, not sure about Mac). The Firefox displays "'".
However, copy-pasting the …
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Hello,
I had panX some weeks ago and it was working perfectly, but I had to run tun the analysis again to add some new sequences. So with my new, larger dataset it does not work anymore.
When I tr…
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Currently we are looking for case counts data and other statistical information from different countries as well as for people who can maintain this data (add, curate, update).
The entire process s…
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I got this error from refine that I struggled to debug:
```
ERROR: SequenceData: loading alignment failed... builds/masked.fasta
ERROR from TreeTime: This error is most likely due to a problem wi…
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I was planning on running multiple scenarios based on distributions of the input parameters to move a way from a deterministic scenarios to quantile projections. This may be more helpful for decision-…
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## The problem
TreeTime has currently a very rudimentary way of resolving polytomies (multi-furcations in the tree).
When this was initially put in place it was never meant to resolve large polyt…