treetime
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neherlab
Maximum likelihood inference of time stamped phylogenies and ancestral reconstruction
## Description I'm tackling the issue of sampling bias in mugration, and was curious if a p-value might be of use here? If I knew the probability of an event...
Is there a way to make analyses reproducible, perhaps by setting a random seed? Specifically, I'm using the ```run``` function of the ```TreeTime``` class to estimate a clock model. I've...
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...
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...
Thanks a lot for this great tool! TreeTime prints implausible leaves to stdout like so: ``` 263.56 TreeTime: The following tips don't fit the clock model, please remove them from...
TreeTime flags leaves that do not conform to the clock model like so: ``` 263.56 TreeTime: The following tips don't fit the clock model, please remove them from the tree....
## 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...
## Issue https://github.com/nextstrain/augur/issues/1057 The monkey pox build has branches where the node distributions are much smaller than the branch distributions and the fft fails as the grid is not coarse...
After reproducing https://github.com/nextstrain/augur/issues/1032 @corneliusroemer and I found that the issue was during `_ml_t_joint`. An internal node was suggested time points that were out of bounds of pre-calculated interpolation objects (`integral_merger_rate`,...
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....
