Tregwiki:FindConservedNoncoding

These programs expect an alignment or sequences and try to find the best-conserved fragments within them:

• Originally, the classical VISTA was used for this, with a cutoff of 70% identity over 100 bp.
• UCSC's most conserved is based on coding regions. Covers 5% of the genome, no configurable threshold.
• Genomic Evolutionary Rate Profiling (GERP) : is only available in perl and does not seem to be threshold-based, it's available on UCSC Encode though
• MCS wants an alignment, a tree, genomic coordiantes for UCSC (bravo!), repeats and exons and a P-Value cutoff value. Nice, but only a webversion.
• gumby expects somewhat less parameters and is downloadable in source (seems to be part of RankVista

Note: When in doubt, prefer multiple alignments (paper)