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Tomas and Sarah will create together a GUI web-service on 6. November.
We will use Twitter's [bootstrap](http://getbootstrap.com) library for that. The GUI will be a middle-ware for obtaining the com…
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In single-rate PTP, the user can disable the Likelihood-Ratio-Test by setting the p-value to 1.
In multi-rate mPTP, there is currently no option available to disable AIC-Testing. Also, if AIC selects…
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Because of problems that emerged with the "small_network" experiments (NetRAX inferring a 0-reticulation network that has better loglikelihood than the "true" simulated network on the simulated MSA da…
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How does the number of partitions influence the number of inferred reticulations?
It is obvious that with LikelihoodType.BEST, network inference on an unpartitioned MSA will always lead to a tree.
…
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I know there exist other programs that can do the conversions. However, it can get very time-consuming to set up an analysis pipeline where each program requires another file format. :-(
Maybe we cou…
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Dear developers,
I would like to know whether it is possible to get a list of best-fitting models for a batch of MSAs. It would be very helpful for phylogenetic applications involving multiple diff…
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Hi,
is there a specific reason why you use the term _memoization_ in the paper, instead of _lookup table_. It could be confusing for the target audience of the paper which, presumably, is made of bioi…
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Now that the columns in the results CSV are fixed (see https://github.com/lutteropp/NetRAX/issues/14), let's list which plots we need. Here are some that I believe make sense to have:
- Use the dat…
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Turns out the order of {reticulationOpt, brlenOpt, modelOpt}, and when and how often to call it during the search is affecting which moves are getting accepted.
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We need an additional experiment that investigates how the brlen-linkage (especially scaled vs. unlinked) affects the NetRAX inference results.