Sarah Lutteropp

I aborted the 30 taxa 3 reticulations run on PhyloDAG since it kept running for ages. Trying with a newly simulated 20 taxa 2 reticulations 4k MSA sites dataset now:...

Very interesting! PhyloDAG on 20 taxa 2 reticulations dataset finished, and it's result sucks really hard: Total runtime: 20.42073 mins Inferred network picture: 

NetRAX results on the PhD laptop for the simulated 20-taxon 2-reticulatiion dataset: - Start from RAxML-NG best ML tree, with LikelihoodModel.AVERAGE: Total inference runtime: 63.0 seconds. Best inferred network has...

I retried PhyloDAG with their default parameters (before I used the parameters stated in their example file). This time, I got: - For the 10 taxa, 1 reticulation, 2k MSA...

RAxML-NG best tree ML inference runtime (starting from 10 random + 10 parsimony trees) on the PhD laptop was: - for 10 taxa, 1 reticulation: 5.688 seconds - for 20...

I hand-wrote the Extended NEWICK for the PhyloDAG network, for the 10 taxa 1 reticulation dataset, using its default parameters: [phylodag_10t1r_inferred_network.txt](https://github.com/lutteropp/NetRAX/files/6986838/phylodag_10t1r_inferred_network.txt)

Re-running PhyloDAG with the same parameters gives me totally different networks every time.

I also started yet another PhyLiNC inference run on the simulated 10 taxa 1 reticulation dataset, this time with telling it that the maximum number of reticulations to try is...

The PhyLiNC output with maximum number of reticulations set to 1, this time without any weird error messages: [phylinc_output_maxret_1.txt](https://github.com/lutteropp/NetRAX/files/6987618/phylinc_output_maxret_1.txt)

The 10 taxa, 1 reticulation dataset: [0_0_msa.txt](https://github.com/lutteropp/NetRAX/files/6987632/0_0_msa.txt) [0_0_partitions.txt](https://github.com/lutteropp/NetRAX/files/6987633/0_0_partitions.txt) [0_0.raxml.bestTree.txt](https://github.com/lutteropp/NetRAX/files/6987631/0_0.raxml.bestTree.txt) [0_0.raxml.startTree.unique.txt](https://github.com/lutteropp/NetRAX/files/6987637/0_0.raxml.startTree.unique.txt) Here are just the network files for the 10 taxa, 1 reticulation dataset: [0_0_true_network.txt](https://github.com/lutteropp/NetRAX/files/6987625/0_0_true_network.txt) [0_0_single_best_inferred_network.txt](https://github.com/lutteropp/NetRAX/files/6987626/0_0_single_best_inferred_network.txt) [0_0_single_average_inferred_network.txt](https://github.com/lutteropp/NetRAX/files/6987627/0_0_single_average_inferred_network.txt) [0_0_multi_best_inferred_network.txt](https://github.com/lutteropp/NetRAX/files/6987629/0_0_multi_best_inferred_network.txt) [0_0_multi_average_inferred_network.txt](https://github.com/lutteropp/NetRAX/files/6987630/0_0_multi_average_inferred_network.txt) [0_0_phylinc_inferred_network.txt](https://github.com/lutteropp/NetRAX/files/6987628/0_0_phylinc_inferred_network.txt) [0_0_phylinc_default_inferred_network.txt](https://github.com/lutteropp/NetRAX/files/6987635/0_0_phylinc_default_inferred_network.txt)...