FigureData.md

• Figure 2: ASTRAL-33%-FAA tree
  • Alignments
  • Gene trees
  • Species tree: in newick, in nexus (first of the three trees)
    • For associated ASTRAL log file, see this.
• Figure 3:
  • Scripts to run the analyses are provided. Moreover, the actual quarter freqencies draw on contracted newick tree files are provided.
• Figures S1-S3:
  • Nexus file: nexus
  • Concatenation alignment used in Figure S2 is given here
  • Plastid tree (S3) is given here.
• Figure S10: Generated using DiscoVista, with inputs given here and outputs given here.
• Figure S11: GC contents
  • Drawn using plot.gc.R
  • Data built using gc-stats.py
  • Figure available here
  • The name of species used in the figure are available here.
• Figure S12: taxon occupancy
  • Figure drawn using this script
  • Data built using this script
  • Figure available here