genetrees

• The main analyses reported in the paper (Figure 2) are based on gene trees given in the Best.33.FAA.tre file.

• We also provide gene trees used in other analyses. File names use these conventions

  • Best.FAA.tre: fully resolved best ML gene trees computed by RAxML on FAA alignments
  • Best.[N].FAA.tre: best ML gene trees on FAA alignments contracted to remove branches with below N% support
  • Best.FNA2AA-C12.tre: fully resolved best ML gene trees computed by RAxML on FNA-2AA-C12 (i.e., AA translated back to DNA with 3rd position removed) alignments

• The following are filtered gene trees (and also supergene trees obtained from statistical binning), used in ASTRAL trees shown in Supplementary Figure S10.

  • binned/Best.FAA.binned.tre
  • binned/Best.FNA2AA-C12.binned.tre
  • filtered/Best.eudicotrsonly.FAA.tre
  • filtered/Best.eudicotrsonly.FNA2AA-C12.tre
  • filtered/Best.removerogoue.FAA.tre
  • filtered/Best.removerogoue.FNA2AA-C12.tre

• The order of gene trees in the files is the order of ls on the genes directory. To be clear, the order is given here.