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How is the ancestral state defined in networks?
If we have the ancestral states for all displayed trees, how do we get the ancestral states for the network? Is it just a weighted average of the per…
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Implement `_mm256_exp_pd()` for computing transition probability matrices (Issue #105 )
The intrinsic does not map to an instruction and is only available in the [Intel Small Vector Library](https://…
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Dear Dr Alexandros
I am trying to implement the AxPARAFIT software that you wrote for my co-evolution analysis. But even after checking the tutorial and data files, I cannot understand the followin…
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I did a profiling run with NetRAX, on a 1000 sites MSA (belonging to a simulated 8 taxon-tree), with 1 random and 1 parsimony starting tree. Turns out that trying arc insertion moves is pretty slow (s…
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Compute an average support/confidence score for the ML tree after a bayesian run.
1. Method:
Sum up the support values for each node of the bayesian tree
- if the corresponding node of the ML tr…
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Dear Sir,
I am using OpenFOAM version v2106 and I cannot compile the solver. It would be really helpful sir if you tell me what OpenFOAM version did you use?
Thank you
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Hello everyone,
if I want to reproject a file with the "rerpoject" command, the following error is shown:
[12:26:22 WARN] The input file uses unsupported non-CityGML namespace(s): http://www.sig…
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I wrote a quick Python script to convert the output of mPTP to a CSV file so that I could use the output with ggmap and with other things where I might want to use the output of mPTP to sort my data i…
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The completed results CSV files from the cluster experiments are finally there.
- small_network: 4-10 taxa, 1-2 reticulations, msa-size either 100*n_trees or 200*n_trees, perfect sampling, linked b…
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@celinescornavacca I've read the part in your book about hardwired/softwired clusters in rooted phylogenetic networks. Now I understand what these are:
- A _cluster_ induced by an edge is the set of …