Examples of running ESPERR to produce Regulatory Potential scores. The Makefile in this directory contains a rule to build a Python virtualenv that contains all of the bx-python and esperr code needed. Just running "make esperr-virtualenv" should get everything set. Subdirectories contain rules for producing scores from specific multiple alignments. Alignments need to be downloaded separately and indexed with maf_build_index.py If you want scores in BigWig format you will also need to have installed UCSC's wigToBigWig and twoBitInfo (or provide the sizes file in some other way).