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@rneher ---
I'm of the opinion that the `augur treetime` module is overly complex. If you just look at the arguments [we see 28 lines](https://github.com/nextstrain/augur/blob/master/bin/augur#L76)…
trvrb updated
6 years ago
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I'm becoming less enthused about BEAST's clock assumptions, and suspect that we may get more stable results by using unrooted trees.
The ever helpful and friendly Andy Magee has supplied us with an…
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**I encounter the following error when using my own newick tree, could you give me some help?**
...
Loading required package: png
Warning message:
replacing previous import 'adegenet::AICc' by 'ph…
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Hi,
I don't think this is the appropriate place to ask this question, but I've been unsure where/who else to ask, and I've been banging my head against the wall for the last few hours.
I have …
ghost updated
6 years ago
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Hi dear team,
I wish to extract the values of the posterior probabilities of states assignments in internal nodes.
I believe these are computed as part of the call to either `SampleAncestors` or…
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There are several processing steps that go into getting a data set ready for BEAST. These are automated in CFT, but given that we want to try variants we have to do them by hand.
#### Install depen…
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A comparison to ML tree reconstruction could potentially be illuminating. We think you could be clearer about what drives the results in your paper. It is unusual for a phylogenetic ancestral reconstr…
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Hi @spond (and @stevenweaver, as this may influence 2.3.7 release timing!),
I believe I have uncovered a SLAC MPI bug:
```
Stephanies-MacBook-Pro:phyphy sjspielman$ mpirun -np 3 /Users/sjspiel…
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When I try to do a `nextstrain/augur` build with a fasta that includes Zika genomes only sampled from the Americas, the build breaks with this error:
`File "../treetime_augur/treetime/treeanc.py"…
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Computing the ancestral sequences as well as ancestral state probabilities of all internal nodes for a given tree. Although this was long implemented in several programs, including very good Tal Pupko…