Changes (in chronological order)
  Files                         Description
  -----                         -----------
  scripts/meme2meme.pl.in       Fixed a bug which was interfering with reading meme text format protein motifs.
  scripts/MotifsUtils.pm        Subroutine intern_to_iupac changed to not use ambiguous characters when describing protein motifs (was resulting in all X).
  src/mast2text.c               Fixed a bug where large residue counts were causing integer overflow.
  etc/tomtom-to-html.xsl        Changed the summary section so the list of motifs is easier to read when there are a lot of motifs.
  --various html--              Fixed a typo that doubled up the '>' after a script tag. The typo had been copied to many files.
  etc/fimo-to-wiggle.xsl        Fixed error in Wiggle format: Ensmble requires variableStep rather than variablestep (note the capitalisation).
  scripts/meme-chip.pl.in       Changed tar creation to tar the parent directory and avoid a tar-bomb.
  scripts/meme-chip.pl.in       MAST and AMA were creating huge files and most people won't need them so they now only run on request.
  src/mast.c                    MAST was failing occasionally on large (> 4Gb) databases due to caching file positions in 32 bit integers which overflowed
  scripts/tamo2meme.pl.in       Fixed handling of identical names.
  src/readseq.c, src/ureadseq.c
    & src/ureadseq.h            Fix to overflow in sequence counter when more than 32767 sequences.
  scripts/MemeWebUtils.pm.in    Avoid calling readseq when file is already in fasta format.
  scripts/MemeWebUtils.pm.in    Improved help/error messages for get_sequence_data.
  website/cgi-bin/
    (meme|tomtom)_request.pl    Replaced call to convert (Image Magick) with gs (Ghostscript). Eventually we won't need Image Magick...
  etc/motif_logo.js             Fixed handling of tab characters at end of last line of the pspm. Now they are trimmed properly.
  -- various perl scripts--     Improved tempfile usage.

Installing the patch:
  1) Change into the root meme_4.6.1 distribution directory
  2) Apply the patch by running:
    patch -p1 -i PATH_TO_PATCH/meme_4.6.1.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.