All data files and scripts to recreate figures from the paper
Script: 01_collection_sites.R
Input: 01_NZ_Rotifer_sites.csv
Output: (ggsave) --> inkscape --> 01_collection_sites.png
IQ-TREE command: bin\iqtree2 -s 02_alignment.phy -B 1000 -nm 3000 -bnni -T AUTO -m MFP
Input: 02_alignment.phy
Outputs: 02_tree.treefile, 02_IQ-tree.log
Script: 03_tree_vis.R
Inputs: 02_tree.treefile, 03_metadata.csv, 03_genus_list.csv
Outputs: supplementary_full_tree.pdf, subtree_{genus}.pdf
Script: 04_barcode_gap_analysis.R
Inputs: 04_metadata_for_barcode_gap.csv, 04_alignment_for_barcode_gap.fasta
Outputs: 04_distmatrix.csv, 04_barcode_gap_results.csv, 04_barcodegap.png
BEAUti priors: 05a_priors.xml
Run this twice in BEAST
Combined the two outputs into one new tree: 05a_ultrametric.tree
Script: 05b_GMYC.R
Input: 05a_ultrametric.tree
Outputs: 05b_species_list.csv, 05b_yulesupport.csv
Note: added the species list column back to the original 03_metadata.csv file and replotted the tree with this information in tip labels