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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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replace the current alignment algorithm with something that tolerates gaps
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In order to perform refactoring and to add new features with more confidence, we need unit, integration and end-to-end tests for:
* algorithm parts. See`src/algorithms`
* React parts - compone…
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There is a growing need for people to assign their sequences to clades and do some simple QC. In the longer term, we also want to support running augur on SARS-CoV-2 data in the cloud. I imagine a col…
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Hello Richard,
Since there is no relaxed clock argument in "rule refine" in Augur, I have tried to separately run Treetime with --relax argument then put the results back to the pipeline as they're…
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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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# 🙋 Feature Request
- In general, make PDF printout more self-explanatory
- Include the help text for variables from the app into the PDF printout
- Choose better names for variables than the…
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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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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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Hi,
I started using treetime recently and some of my trees look like this, while the others look fine. My sample size is 25 and here is an example code that I used.
`treetime --tree VREst18_clonalfr…