Datasets

Two-phase experiment simulated DNA datasets README

There are 84 model conditions, with either 1000, 500, or 100 taxa, and either long, medium, or short gap length types. Each model condition is referred to with the string "<number of taxa><gap length type: L for long, M for medium, S for short>-<id number>".
Each model condition has 20 replicate datasets.
For each model condition, an associated link to a tarball is listed below. The tarball contains the 20 replicate datasets for that model condition.
After decompressing a tarball, the directory structure <model condition name>/R<replicate number>/ will have the following files:

rose.tt - Potentially Inferrable Model Tree, or PIMT, (model tree with zero event edges collapsed) in Newick format
rose.mt - binary model tree in Newick format
rose.aln.true.fasta - true alignment in FASTA format
rose.mt.internal - binary model tree with all nodes named in Newick format
rose.aln.true.internal.fasta - true alignment for all nodes' sequences in FASTA format

1000 long	1000 medium	1000 short	500 long	500 medium	500 short	100 long	100 medium	100 short
1000L-1 1000L-2 1000L-3 1000L-4 1000L-5 1000L-6 1000L-7 1000L-8 1000L-9 1000L-10	1000M-1 1000M-2 1000M-3 1000M-4 1000M-5 1000M-6 1000M-7 1000M-8	1000S-1 1000S-2 1000S-3 1000S-4 1000S-5 1000S-6 1000S-7 1000S-8 1000S-9 1000S-10	500L-1 500L-2 500L-3 500L-4 500L-5 500L-6 500L-7 500L-8 500L-9 500L-10	500M-1 500M-2 500M-3 500M-4 500M-5 500M-6 500M-7 500M-8	500S-1 500S-2 500S-3 500S-4 500S-5 500S-6 500S-7 500S-8 500S-9 500S-10	100L-1 100L-2 100L-3 100L-4 100L-5 100L-6 100L-7 100L-8 100L-9 100L-10	100M-1 100M-2 100M-3 100M-4 100M-5 100M-6 100M-7 100M-8	100S-1 100S-2 100S-3 100S-4 100S-5 100S-6 100S-7 100S-8 100S-9 100S-10