Supporting data for: The danger zone: the joint trap of incomplete lineage sorting and long-branch attraction in resolving the Gondwanan origin of Rafflesiaceae and Apodanthaceae

This is supporting sequence data for the paper: The danger zone: the joint trap of incomplete lineage sorting and long-branch attraction in resolving the Gondwanan origin of Rafflesiaceae and Apodanthaceae. It contains DNA and protein sequences as well as gene trees for 2135 loci for the investigation of the phylogenetic placement of the parasitic Rafflesiaceae and Apodannthaceae. Three datasets were included: Data S1 Sequence alignments and gene trees for the 2135 loci analyzed in the study. The lists of loci included in the data subsets G446 and G829 are also provided. Both the raw alignments and masked alignments by HmmCleaner are provided for DNA and protein sequences. Each gene has 5 sets of gene trees inferred using different models in IQTREE:(1) *.GTR_codon.treefile: codon-based partition within gene (first, second, third codon in separate partitions) + forcing GTR (no +I or +R or +G); (2) *.MFP_codon.treefile: codon-based partition within gene + ModelFinder best fitting model; (3) *.msetGTR.treefile: no partition within gene + forcing GTR (with +I or +R or +G); (4) *.msetGTR_codon.treefile: codon-based partition within gene + forcing GTR (with +I or +R or +G); (5) *.na.mask.fas.treefile: no partition within gene + ModelFinder best fitting model. Data S2 Species tree in newick format generated by the 22 analyses described in Cai et al. Table 1 and Appendix S9. For partition-based concatenation analyses, the best partition and substitution scheme in nexus format from IQ-TREE is also provided.The program and command line used to generate these species trees can be found on GitHub: https://github.com/lmcai/Rafflesiaceae_phylogenomics/tree/master/4_phylogeny_hypo_generation Data S3 Log Likelihood per gene, log Likelihood per site, and rate per site estimated from the concatenated DNA sequence of the complete dataset. These likelihoods and rates are used for AU tests in Appendix S13 and the rate-sensitivity analysis in Figure 2.