Simulated CRE data for the manuscript
"REforge associates transcription factor binding site divergence in regulatory elements with phenotypic differences between species"
by Langer, Roscito, and Hiller 2018.


The directory contains
- 10000backgroundCREs.tar.gz				Background CREs where every branch in the phylogeny evolved under selection to preserve the target regulatory activity. Regulatory activity is controlled by TF set 1.
- 5000backgroundCREs.differentMotifs.tar.gz		Background CREs where every branch in the phylogeny evolved under selection to preserve the target regulatory activity. Regulatory activity is controlled by 5 different activator TFs (set 2).
- 200foregroundCREs.0.03subssite.tar.gz			Tissue-specific foreground CREs where the three trait-loss branches evolved neutrally for 0.03 subs. per site.  
- 200foregroundCREs.0.06subssite.tar.gz			Tissue-specific foreground CREs where the three trait-loss branches evolved neutrally for 0.06 subs. per site.  
- 200foregroundCREs.0.09subssite.tar.gz			Tissue-specific foreground CREs where the three trait-loss branches evolved neutrally for 0.09 subs. per site.  
- 200foregroundCREs.pleiotropic.0.03subssite.tar.gz	Pleiotropic foreground CREs where the three trait-loss branches evolved without selection to preserve activity in tissue 1 for 0.03 subs. per site.  
- 200foregroundCREs.pleiotropic.0.06subssite.tar.gz	Pleiotropic foreground CREs where the three trait-loss branches evolved without selection to preserve activity in tissue 1 for 0.06 subs. per site.  
- 200foregroundCREs.pleiotropic.0.09subssite.tar.gz	Pleiotropic foreground CREs where the three trait-loss branches evolved without selection to preserve activity in tissue 1 for 0.08 subs. per site.  
- activatorTFMotifs.set1.lib				TF motifs used to create the 10000 background and all foreground CREs.
- activatorTFMotifs.set2.lib				TF motifs used to create the 5000 background CREs.
- tree.nh						Phylogenetic tree.

Each tar.gz file contains a directory with one multi-fasta file for each CRE.
Each multi-fasta file contains the sequence of all internal and terminal nodes in the phylogenetic tree.