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https://en.wikipedia.org/wiki/Basal_(phylogenetics) presents basal as if some contemporary tips are closer to the root than others. Revise to indicate that basal means closer to the base of the tree (…
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The term homoeologous should be a child of homologous, sibling of paralogous and orthologous. It means (by analogy to existing descriptions), "An attribute describing a kind of homology where divergen…
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la funcion compare en ete3 y funciona bien si el arbol no tiene duplicaciones o tiene duplicaciones normales, pero casca cuando tiene duplicaciones especificas para una especie.
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See Lindsay's Python notebook for a demo on running pkasolver.
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- Joëlle Barido-Sottani (Iowa State University)
- https://cran.r-project.org/package=FossilSim on CRAN, https://github.com/fossilsim/fossilsim for the development version (GPL-3 license)
- FossilSim…
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When tracking phylogenies in real time, we often end up with extant (i.e. alive) taxa that are not leaf nodes. Some (possibly most or all?) bioinformatics and paleontology tools represent this scenari…
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It's not 1-to-1 in nature. See #8 for how this can bite us.
## Lewontin paradox
* Abundance doesn't equal Ne. Model Ne directly (see below), or impose "density dependence" on Ne?
* What if we con…
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To get rid of a large number of dependencies and make it easier to maintain and extend the kernel function, I've reimplemented the kernel in R. As expected, it is slower than the original C-igraph im…
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Hi @Pbdas
I ran `./pipeline/9_mptp_on_all_trees.py work_dir/2021-11-19_00/fmsan/` and I got following error on my terminal
WARNING: delimit was not compiled with libgsl. Likelihood ratio test …
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In GitLab by @pmoret on Apr 12, 2016, 15:12
```sql
-- Homologous genes have a same omaGroupId. They can be retrieved at a given taxon.
CREATE TABLE
OMAHierarchicalGroupToGeneAndTaxon (
omaGroup…