A robustly rooted tree of eukaryotes reveals their excavate ancestry [Data]

Supplementary data for the manuscript: "A robustly rooted tree of eukaryotes reveals their excavate ancestry"
Folder/file descriptions:

Single protein datasets - unaligned: contains unaligned protein sequences in FASTA format for all individual marker proteins
Single protein datasets - aligned: contains protein sequences in FASTA format for all individual marker proteins after alignment with PREQUAL and MAFFT
Single proteins datasets - aligned and trimmed: contains protein sequences in FASTA format for all individual marker proteins after alignment with PREQUAL and MAFFT and trimming with BMGE
Models: contains all phylogenetic models generated for this study
Scripts: contains all custom scripts
Phylogenomic supermatrices: contains all phylogenomic supermatrices used for all analyses
Anae+ phylogenetic trees: contains all phylogenetic trees estimated from the concatenated dataset that includes Anaeramoeba (Anae+)
Anae- phylogenetic trees: contains all phylogenetic trees estimated from the concatenated dataset that does not include Anaeramoeba (Anae-)
Simulated Alignments With Gaps: contains 100 alignments simulated from the consensus tree (OpiDip+/Anaeramoeba) with the gap pattern from the original alignment preserved
Simulated Alignments Without Gaps: contains 100 alignments simulated from the consensus tree (OpiDip+/Anaeramoeba) with no gaps
Hemimastix_sequences.fasta: FASTA file of all sequences from Hemimastix kukwesjijk used in the final dataset analyses