Changes
  Files                         Description
  -----                         -----------
  website/cgi-bin/meme-chip.pl  Changed the command lines for the programs that use MEME output to use meme text format.
  etc/meme-chip.txt             Changed the meme-chip script to allow for program failure and report it to the user.
  src/ame.c                     Fixed 3 bugs:
                                  Bug 1:  highest_score was incorrect scope, so it unneccessarily performed statistical 
                                          tests in cases where no motif hits were found in sequences.
                                  Bug 2:  In the case of a motif with no hits, it left the score NULL rather than 1. 
                                  Bug 3:  Some diagnostics run with --verbose 5 reported the wrong motif name (but correct 
                                  scores), as the ordering of reverse complement motifs has changed since AME was originally written.
                                  

Installing the patch:
  1) Change into the root meme_4.6.0 distribution directory
  2) Apply the patch by running:
    patch -p0 -i PATH_TO_PATCH/meme_4.6.0.patch_1
  3) Make the install files:
    make
  3) Install by running:
    make install

  If run on split server (separate Apache and Tomcat servers) this patch needs to be
  applied to both sides.