There are nine model conditions in total characterized by

the number of genes
  +  25  (5 complete, 20 incomplete)
  +  50  (10 complete, 40 incomplete)
  +  100 (25 complete, 75 incomplete)
  +  200 (50 complete, 150 incomplete)

and the level of ILS
  +  moderate (10M)
  +  high (2M)
  +  very high (500K)

For each model condition, there are 20 replicates datasets with directories containing the following files where N is the number of genes:
  +  true species tree (true-species.tre)
  +  N true gene trees (true-genes.tre)
  +  N estimated gene trees (raxml-genes.tre)
  +  species tree estimated using ASTRID (astrid.tre)
  +  N gene trees completed using ASTRAL-II (completed-astral-raxml-genes.tre)
  +  N gene trees completed using OCTAL with ASTRID (completed-octal-astrid-raxml-genes.tre)

The 200 gene 10M and 2M directories include the following additional files:
  +  species tree estimated using ASTRAL (astral.tre)
  +  greedy consensus tree of the complete, estimated gene trees (greedy.tre)
  +  random tree on complete taxon set (random_tree.tre)
  +  200 gene trees completed using OCTAL with ASTRAL (completed-octal-astral-raxml-genes.tre)
  +  200 gene trees completed using OCTAL with greedy consensus (completed-octal-greedy-raxml-genes.tre)
  +  200 gene trees completed using OCTAL with random tree (completed-octal-random_tree-raxml-genes.tre)
  +  200 gene trees completed using OCTAL with true species tree (completed-octal-true-species-raxml-genes.tre)

The 200 gene directories also include lists of the genes sampled from the original 1000-gene datasets (full-subset-genes.txt, missing-subset-genes.txt). These can be used to obtain the original alignment files from the ASTRAL-II study (https://sites.google.com/eng.ucsd.edu/datasets/astral-ii). In particular, see the following files: alignments-200taxon-10M.tar.bz, alignments-200taxon-2M.tar.bz, and alignments-200taxon-500K.tar.bz.

NOTE: The 25, 50, and 100 gene directories contain subsets of the 200 gene trees from the corresponding ILS condition so there are no additional alignment files for these conditions. Specifically, for the 25 gene condition was created by taking the first 5 complete genes are the first 20 incomplete genes from the model condition with 200 genes.