CRE data for the manuscript
"TFforge utilizes large-scale binding site divergence to identify transcriptional regulators involved in phenpotypic differences"
by Langer and Hiller 2018.


The directory contains
- 1000foregroundCREs.0.03subssite.tar.gz		Type 1 CREs. Foreground CREs where the three trait-loss branches evolved neutrally for 0.03 subs. per site.  
- 1000foregroundCREs.0.06subssite.tar.gz		Type 1 CREs. Foreground CREs where the three trait-loss branches evolved neutrally for 0.06 subs. per site.  
- 1000foregroundCREs.0.09subssite.tar.gz		Type 1 CREs. Foreground CREs where the three trait-loss branches evolved neutrally for 0.09 subs. per site. 
- 1000backgroundCREs.tar.gz				Type 2 CREs. 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.
- 1000backgroundCREs.differentMotifs.tar.gz		Type 3 CREs. 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).
- 1000foregroundCREs.pleiotropic.0.03subssite.tar.gz	Type 1 CREs. Pleiotropic foreground CREs where the three trait-loss branches evolved without selection to preserve activity in tissue 1 for 0.03 subs. per site.  
- 1000foregroundCREs.pleiotropic.0.06subssite.tar.gz	Type 1 CREs. Pleiotropic foreground CREs where the three trait-loss branches evolved without selection to preserve activity in tissue 1 for 0.06 subs. per site.  
- 1000foregroundCREs.pleiotropic.0.09subssite.tar.gz	Type 1 CREs. Pleiotropic foreground CREs where the three trait-loss branches evolved without selection to preserve activity in tissue 1 for 0.09 subs. per site.  
- tree.nh						Phylogenetic tree.
- Crx.bed						mm10 coordinates of analysed Crx peaks overlapping conserved regions
- Nrl.bed						mm10 coordinates of analysed Nrl peaks overlapping conserved regions

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.