This repo contains MSAs from TreeBASE which we downloaded for our experiments, and - for most MSAs - the best trees we found after 100 RAxML-NG tree searches under the "GTR+G" model for DNA and "LG" model for AA MSAs (with their respective inferred model parameters). We substituted the original taxon names since some of them were quite creative and made the parsers in the software we had to use for our experiments cry.
There is also a SQLite database with our example scripts here, that can be used for easier lookup of MSAs.
-
Piel, W. H., Chan, L., Dominus, M. J., Ruan, J., Vos, R. A., and V. Tannen (2009) TreeBASE v. 2: A Database of Phylogenetic Knowledge. e-BioSphere 2009.
-
Vos, R. A., Balhoff, J. P., Caravas, J. A., Holder, M. T., Lapp, H. Maddison, W. P., Midford, P. E., Priyam, A., Sukumaran, J., Xia, X. and A. Stoltzfus (2012) NeXML: rich, extensible, and verifiable representation of comparative data and metadata. Systematic Biology 61(4): 675-689.
-
Alexey M. Kozlov, Diego Darriba, Tomáš Flouri, Benoit Morel, and Alexandros Stamatakis (2019) RAxML-NG: A fast, scalable, and user-friendly tool for maximum likelihood phylogenetic inference. Bioinformatics, 35 (21), 4453-4455 doi:10.1093/bioinformatics/btz305