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In this likelihood model, we only use the loglikelihood of a single displayed tree in the network, made smaller by multiplying it by the probability of that displayed tree. This kinda tells us that Li…
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> Hello,
> I was wondering whether it is among your plans (and whether it is possible to implement) to add protein mixture models to RaxML, particularly C10-C60 (http://bioinformatics.oxfordjournals.o…
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### Confirm that this is a metadata correction
- [X] I want to file corrections to make the metadata match the PDF file hosted on the ACL Anthology.
### Anthology ID
2024.bea-1.51
### Type of Pape…
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Currently, branch length optimization is where most of the NetRAX runtime is spent.
I was wondering:
If we change a single branch length, do we need to care about loglikelihood changes in the rest…
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Naively, one would store `number_of_network_nodes * number_of_displayed_trees` CLV vectors. However, there are regions in the network that are exactly the same over multiple displayed trees. Those reg…
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With the current horizontal rNNI and rSPR moves, can we place a reticulation somewhere else **in a single step**?
I think no... It looks to me that we can only change one of the parents of a reticu…
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Perhaps now it would be a good idea to decide the data types of the following `pll_partition_t` variables:
| **type** | **Variable** | **Role** | Suggested type |
| --- | --- | --- | --- |
| `int` | …
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In the text, you will find my comments. Please use Adobe Reader to see them
[NetRAX___Phylogenetic_Network_Inference.pdf](https://github.com/lutteropp/NetRAX/files/5519440/NetRAX___Phylogenetic_Ne…
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Hello,
I am using RAxML-NG to generate ancestral trees for my exon sequences derived from eukaryotic genomes. My workflow is as follows:
```
raxml-ng --msa $MSA_FILE --data-type DNA \
--se…