Sarah Lutteropp

I hate extra work, but it would be awesome if we would also compare with SNAQ, PhyloNet ML, and PhyloNet PseudoML on our simulated data. Instead of a MSA, these...

First, the per-gene MSAs, built through variations of this very nice and useful command: `awk '{if(/^>/)print $0; else print substr($0,1,1000)}' 20t_2r_msa.txt > 20t_2r_gene1_msa.txt` For the 10 taxa, 1 reticulation dataset:...

These are the "gene trees" inferred by RAxML-NG, and the logfiles: For the 10 taxa, 1 reticulation dataset: [10t_1r_gene2_msa.txt.raxml.bestTree.txt](https://github.com/lutteropp/NetRAX/files/6987734/10t_1r_gene2_msa.txt.raxml.bestTree.txt) [10t_1r_gene1_msa.txt.raxml.bestTree.txt](https://github.com/lutteropp/NetRAX/files/6987736/10t_1r_gene1_msa.txt.raxml.bestTree.txt) [10t_1r_gene2_msa.txt.raxml.log.txt](https://github.com/lutteropp/NetRAX/files/6987733/10t_1r_gene2_msa.txt.raxml.log.txt) [10t_1r_gene1_msa.txt.raxml.log.txt](https://github.com/lutteropp/NetRAX/files/6987735/10t_1r_gene1_msa.txt.raxml.log.txt) For the 20 taxa, 2 reticulations dataset: [20t_2r_gene4_msa.txt.raxml.bestTree.txt](https://github.com/lutteropp/NetRAX/files/6987724/20t_2r_gene4_msa.txt.raxml.bestTree.txt)...

Apparently SNAQ requires a set of gene trees in 1 file, and 1 start tree. So here's the input data for SNAQ: - For the 10 taxa, 1 reticulation dataset:...

Here are the SNAQ results for the 10 taxa 1 reticulation dataset. - SNAQ output for 10 runs, trying for at most 1 reticulation: [snaq_results_10t_1r_maxret_1.zip](https://github.com/lutteropp/NetRAX/files/6988001/snaq_results_10t_1r_maxret_1.zip) Elapsed time: 4898.73 seconds, 10...

- SNAQ output for 10 runs, trying for at most 2 reticulations: [snaq_results_10t_1r_maxret_2.zip](https://github.com/lutteropp/NetRAX/files/6988213/snaq_results_10t_1r_maxret_2.zip) Elapsed time: 7489.32 seconds, 10 attempted runs Here again just the network: [inferred_network_snaq_10t_1r_maxret2.txt](https://github.com/lutteropp/NetRAX/files/6988217/inferred_network_snaq_10t_1r_maxret2.txt) Since SNAQ inferred a...

Turns out both SNAQ and PhyLiNC overestimate the number of reticulations if I tell them to try for at most 2 reticulations.

NEXUS Submission files for PhyloNET, for the 10 taxa 1 reticulation dataset: [10_1r_phylonet_submission_files.zip](https://github.com/lutteropp/NetRAX/files/6988431/10_1r_phylonet_submission_files.zip)

PhyloNET MPL (Maximum Pseudolikelihood) results for the 10 taxa 1 reticulation dataset: - With max_reticulations = 1: [10t_1r_phylonet_maxret_1_mpl_output.txt](https://github.com/lutteropp/NetRAX/files/6988438/10t_1r_phylonet_maxret_1_mpl_output.txt) [10t_1r_phylonet_maxret_1_mpl_inferred_network.txt](https://github.com/lutteropp/NetRAX/files/6988439/10t_1r_phylonet_maxret_1_mpl_inferred_network.txt) Inferred a 1-reticulation network, total inference runtime on PhD laptop: 158...

The judge results, for all networks on the 10 taxa 1 reticulation dataset we have so far: (with SNAQ, I had to manually fix the inferred 2-reticulation network that had...