This directory contains exemplary data from the neotrop data set mentioned in the paper. It was obtained from [1].
Setting up the directory:
tar xzvf neotrop.tar.gz
This dataset contains a reference tree (tree.newick) and reference alignment (reference.fasta).
Two query files are provided: one with 10,000 aligned query sequences (query_10k.fasta, 46MB) and one with 100,000 aligned query sequences (query_100k.fasta, 457MB).
Additinally I have provided a file called infofile. This is one way of passing model parameters to EPA-ng, as these parameters are not re-inferred in the program itself.
To create this file I ran RAxML-8 with the -f e option which computes and outputs the model parameters in the RAxML_info.* file.
mkdir result
../../../bin/epa-ng --tree tree.newick --ref-msa reference.fasta --query query_10k.fasta --model infofile --outdir result
[1] Mahé, F., de Vargas, C., Bass, D., Czech, L., Stamatakis, A., Lara, E., Singer, D., Mayor, J., Bunge, J., Sernaker, S. and Siemensmeyer, T., 2017. Parasites dominate hyperdiverse soil protist communities in Neotropical rainforests. Nature ecology & evolution, 1(4), p.0091.