phyloscan logo software for locating sequence motifs in promoter regions
Monday December 22, 2014

Optional: e-mail notification of results to:
(e-mail addresses are not used for any other purpose)
Paste in a Newick format phylogentic tree:
Or upload a file containing a Newick format tree:
Select a format for the promoter sequences:    Want more formats?

Paste in aligned promoter sequences to be scanned:

Or click here to use the 2 MB Carmack et al. (2007) data set. (May take a few seconds each to load, clear, and submit.)
Or upload a multi-species alignment file:
Select a format for the motif model:

Paste in the motif model:

Or click here for motif model databases.
Or upload a file containing a motif model:
Motif model is palindromic
Fragmentation mask of motif model ('*' means position is included and '.' means position is ignored)
p-value cutoff used for initial screening of transcription factor binding sites
q-value cutoff for reporting significant results
Enter site rank weights as space separated numbers:

Phyloscan v2.2.c - Brown University Center for Computational Molecular Biology
If you use Phyloscan, please cite us.