Sarah Lutteropp

I had to redo experiment D, here is the new result file [D_scramble_results.csv](https://github.com/lutteropp/NetRAX/files/6887182/D_scramble_results.csv)

Result file for experiment F, including number of MSA patterns [F_mpi_results.csv](https://github.com/lutteropp/NetRAX/files/6894528/F_mpi_results.csv)

Results for the second experiment F, with more MSA patterns and more MPI processes [F_mpi_results2.csv](https://github.com/lutteropp/NetRAX/files/6899801/F_mpi_results2.csv)

Detailed RAxML-NG output on the high fraction of invariant sites per gene attached. The genes have between twenty-something and one-hundred-something MSA patterns. [raxml_snakes_sites_report.txt](https://github.com/lutteropp/NetRAX/files/6950732/raxml_snakes_sites_report.txt)

This is the partitioned MSA I created for use with NetRAX, using [this](https://github.com/lutteropp/NetRAX/blob/master/experiments/assemble_snakes/nexus_to_fasta.py) and [this](https://github.com/lutteropp/NetRAX/blob/master/experiments/assemble_snakes/fasta_files_to_concat.py) quick little script I wrote: [snakes_for_netrax.zip](https://github.com/lutteropp/NetRAX/files/6950857/snakes_for_netrax.zip)

I want to run NetRAX on this dataset, using the phobos lab cluster. I am doing different search variants: - Start from RAxML-NG best ML tree, with LikelihoodModel.BEST - Start...

TODOs listed by @celinescornavacca in the Slack channel: - [x] find out the kind of sequences they use - [x] write the newick for their network - [x] write the...

>find out the kind of sequences they use From [this](https://academic.oup.com/sysbio/article/67/5/743/4925328) paper: "Anchored hybrid enrichment data were generated and aligned in Chen et al. (2017) following the procedures of Lemmon et...

NetRAX results on the phobos lab cluster for the snakes dataset: - Start from RAxML-NG best ML tree, with LikelihoodModel.AVERAGE: Total inference runtime: 844.0 seconds. Best inferred network has 1...

@celinescornavacca I figured out where this 2-reticulation network from the thesis comes from. It says it comes from the SNAQ inference from the paper, but the paper clearly says that...