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Hello,
I have been using Pangolin to evaluate my tool on a simulated dataset.
However, I cannot get the lineage that I expect with pangolin. I would be glad if you could have a look why that cou…
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e.g., I just got the following messages:
```
2024-05-14T17:00:35.209125Z [info ] Starting pipeline as_of_date=2024-05-14 filename=assign_clades.py lineno=193 run_time=20240514T130…
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This call
```R
taxize::downstream('Brassicaceae', db='ncbi', downto='genus')
```
loses all descendents of the clade 'Brassicaceae incertae sedis'. I believe this clade gets filtered out as amb…
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### Context
Requested by @trvrb in today's [forecasting-automation meeting](https://docs.google.com/document/d/1rRLRQmwhVOjRRdA4KUkh37gv3i5VbO9pcZk4MLa8eiQ/edit#heading=h.f31o8y1x359u):
> Separate…
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Here's an idea we just came up with over beers.
One thing that would be useful to know is, given any summary tree, which splits on that tree are most problematic. Obviously the posterior support is …
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In my beast.xml (attached), I have MRCA priors set up in a consistent manner, but due to the implementation of `SimpleRandomTree`, the initialization fails.
At its core, I have the following stack …
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This is a new warning being generated by the tests, and I don't think there are actually should be collinear variables here so I'm not sure what's happening.
``` r
suppressPackageStartupMessages(l…
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Hi @rhysnewell,
I run some dD/dS calculation via the following command:
lorikeet consensus --interleaved ../01B.trimmed_reads/S138_R1.CoupledReads.fa.gz --reference ../OMZ_SAG_HQ_clades_Ic_analy…
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Clades, whether using a maximum or minimum clade definition, may be defined as [crown-clades](https://en.wikipedia.org/wiki/Crown_group) or [total clades](https://en.wikipedia.org/wiki/Crown_group#Pan…
hlapp updated
3 years ago