NetRAX
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lutteropp
Phylogenetic Network Inference without ILS
I am trying to run NetRAX on simple example data posted in your website: https://github.com/lutteropp/NetRAX/files/6986406/datasets_phylinc_exp_smaller.zip. Installation seems to go smoothly. However, when I try to run like: mpiexec ./netrax --msa...
Thank you for writing and sharing such a great program! I am using NetRAX to analyze some viral datasets (~10 taxa, ~150kbp), but I have had some difficulty getting the...
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, 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...
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...
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_Network_Inference.pdf) I want to stress here that our definition 3 correspond to Eq 4 in...
Still coming: - all_brlen_linkage_results - all_standard_random_results - all_standard_multi_results - (... likely some more) [all_prob_results.csv](https://github.com/lutteropp/NetRAX/files/6693483/all_prob_results.csv) [all_scaler_results.csv](https://github.com/lutteropp/NetRAX/files/6693485/all_scaler_results.csv) [all_unpartitioned_results.csv](https://github.com/lutteropp/NetRAX/files/6693486/all_unpartitioned_results.csv) [all_standard_results.csv](https://github.com/lutteropp/NetRAX/files/6693487/all_standard_results.csv)
We want to run NetRAX on this empirical dataset (from https://advances.sciencemag.org/content/5/5/eaav9188) which is available for download at https://bioweb.supagro.inra.fr/WheatRelativeHistory/index.php?menu=download - We need the IndividualAlignments data, which we merge together into one...
For all experiments, we will have (unless mentioned otherwise): - number of MSA sites = 1000 * (number of displayed trees) - perfect sampling: sites are sampled proportionally to the...