2017-10-14-Leache-4spp-seqs.zip and 2017-10-14-Leache-10spp-seqs.zip contain directories for each scenario.
ABCD-EFGH_0p01 means migration at rate 0.01 between branches ABCD and EFGH.
E-F_E-G_E-H_F-G_F-H_G-H_1p0 means migration at rate 1.0 between 6 pairs of branches.
F-G-1-allele means a single allele transferred from F to G at time zero. F-G-1-mig means a single individual transferred from F to G at time zero.
COAL or NoMig means the same thing: coalescence only, or no migration. The time-zero scenarios are derived from these, by renaming a sequence or sequences.
Inside these are directories per replicate, containing the sequence files and other files.
ctrl.txt is the BPP control file, seq.txt is the sequences.
These two files are in all scenarios. Scenarios other than the time-zero ones also have Imap.txt (of little interest), trees.txt, the gene trees, and migs.txt, which provides information about the individual migrations.