Sarah Lutteropp

- extra table - extra array - extra tree Extra outputs are like in the Booster tool. Usage like this: `./raxml-ng --support --tree primREF.nw --bs-trees primBOOT.nw --bs-metric TBE --extra tbe_extra_table,tbe_extra_array,tbe_extra_tree,tbe-cutoff{0.3}...

Support species synonyms

2

Hi, currently, species genomes are not found by the biomartr package if I search for a species synonym. For example: `is.genome.available("Kluyveromyces thermotolerans", db="refseq")` returns FALSE, but `is.genome.available("Lachancea thermotolerans", db="refseq")` returns...

Support genome retrieval for misclassified species

2

Hi, I encountered a weird behavior: `is.genome.available("Candida glabrata", db = "genbank")` returns TRUE, but `getGenome(db = "genbank", organism = "Candida glabrata")` claims that "No reference genome or representative genome was...

Feature Request: Build FM index for a set of strings

1

Hello, I want to use the csa_wt index for counting DNA-substrings of variable size in a file containing DNA sequencing reads. The file looks like this, i.e. the reads are...

[Quartet_based_computations_of_internode_certainty_provide_accurate_and_robust_measures_of_phylogenetic_incongruence___Supplementary_Material(2).pdf](https://github.com/lutteropp/QuartetScores/files/3739895/Quartet_based_computations_of_internode_certainty_provide_accurate_and_robust_measures_of_phylogenetic_incongruence___Supplementary_Material.2.pdf)

There might be a bug in case of rooted reference tree (`tree.root_node().rank() == 1`): In Debug mode, the assertion `assert(id < quartet_lookup_.size())` in quartet_lookup_table.hpp fails. Reason according to @sgiesse: unrooted:...

Comparison with PhyLiNC, PhyloDAG, SNAQ, PhyloNET MPL, and PhyloNET ML on simulated data

34

The complete PhyLiNC output for a simulated 10 taxon 1 reticulation 2000 MSA sites dataset, on the PhD laptop. I set the maximum number of reticulations it should try to...

Detailed Future Work Ideas

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Detailed future work ideas, such that we can remove them from the supplement: \section{Detailed Future Work Ideas} \subsection{Runtime Improvements} \subsubsection{Improve virtual re-rooting during Branch-Length Optimization} Currently, we always reroot back...

Snakes Empirical Dataset

18

I have found an empirical snakes dataset mentioned in [this](https://www.proquest.com/openview/441a5ca05598dd8ecefd5948681a22d0/) dissertation, on page 56. Allen-Savietta compares her model for evolutionary rate estimation with the evolutionary rates on this dataset. She...

TODO: Compare current implementation with this pseudocode: \section{Pseudcodes for Nontopology Optimization} \begin{algorithm} \DontPrintSemicolon \KwIn{The current network $annNetwork$ with parameter vector $\vartheta$; the optimization type $type$.} \KwOut{The current network, with optimized...