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Aim:
Production grade library for pathogen phylodynamics
Ideas:
* XMl wrappers for safe model building in BEAST
* bacterial phylodynamics module:
* species specific configurations / workf…
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I'm finding the time and population size conversions in the sweeps model super confusing, and I would *really* like to decouple the trajectory simulation from the sweep definition. I don't think this …
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As this project moves forward, it might be helpful to have some standard ways to modify simulation output to add noise and error to the data. Some of these would require changing the simulation proces…
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Hello Joe,
I have noted that when using a custom network hybrid-Lambda generates gene trees where the hybrid edge "detaches" and becomes a leaf, that is, for the network including the hybrid edge h…
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@awohns has tried a new approach to inferring tree sequences with ancients, where all samples (modern and ancients) are simply added to a SampleData file and the tree seq is inferred. This appears to …
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Dear Cai,
I want to use your scripts to test my data. I used python 3 and R v. 4. I have installed all the packages your scripts suggested.
However, when I use the following command to run…
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Hi
I am working with the SMC++ and having issue in understanding the Watterson's estimate of theta.
By looking at the code,
theta = 2*N0*(mu)
0.0001 = 2*N0*(mu)
so estimate of theta is alr…
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I want a function that will remove the topology after (forwards in time) a specific time, and mark each extant lineage with as a sample. The intuition is that we're drawing a line accross the tees, an…
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We can attempt to infer a variable Ne by performing a tsdate inference, assessing the coalescence distribution over time (possibly broken up by population, if necessary), then using a rescaled set of …
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As far as I can see the only way to set up a binary ctmc or covarion analysis in BEAUTi is to use the included templates. This makes it hard to use a different template (e.g. MultiTypeTree or somethin…