July 19, 2011: fixed a display bug in mi_draw_matrix_html.pl as log(p) should
actually just be p (thank you to Marc Chatenay-Lapointe, who noticed the error); fixed a memory leak (regex.c); fixed a display issue if multiple expression bins have the same range (mi_summarize.pl); adds support for multiple AlignACE name matches for each motif, protein array hits; adds dooptimizetowm and dooptimizetoextend to fire.pl; should contain current iGET updates (btsui)

August 24, 2010: fixed a bug in fire.pl affecting the RNA quantization of
continuous data if an ebins value was specified; the ebins parameter is now
taken into account (btsui)

August 11, 2010: fixed a small bug in the Pearson correlation calculation;
negative values are no longer zero (btsui)

July 24, 2009: added support for rice (requested by Arjun Krishnan, VTech)

February 5, 2009: added the poplar to the list of supported species (following
 a request by Olivia Wilkins, U of Toronto)

November 22, 2008: fixed a small regexp bug in FIRE_analyze_input_files.pl (thank you
 to Eric Jungwoo Suh, Princeton Univ, for reporting it).

November 20, 2008: new release. Improved installation, portability, cleaned up
  the code, removed warnings, improved overall robustness. 

July 11, 2008: this new version fixed a whole bunch of small things. Thanks to Yael Altuvia
  (Hebrew University) for reporting a small bug in the quantization procedure.

Feb 26, 2008: modified diverse parts of the source code so that the code
  compiles on Solaris. Thanks a lot to Jenny Barna (University of Cambridge) 
  for feedback and help.

Dec 24, 2007: we now use the autotools to configure, compile and package FIRE.
  The new compilation instructions are described in the FIRE tutorial
  (http://tavazoielab.princeton.edu/FIRE/tutorial.html)


Dec 15, 2007: we have added support for S. bayanus. This was done by Konrad Karczewski, 
  one of our talented and ultra-motivated Princeton undergrads.

  Use it with --species=bayanus (or --species=bayanusmid and
  --species=bayanushigh for longer sequences).


Dec 13, 2007: we have added support for gapped motifs in FIRE. However, the
  gap size has to be specified in advance.

  To search for gapped motifs, use the option --gap=N when running fire.pl.
  When looking for gapped motifs, it is preferable to use the option --k=6 instead of the
  default --k=7 (--gap=6 --k=6 will look for motifs of the form XXX......XXX).
  

Dec 8, 2007: following a request by Dave Burt (Roslin Institute, UK), we added support 
  for chicken. We used ENSEMBL transcript identifiers as default identifiers (RefSeq 
  sequences are also provided in chicken_data.zip). 

  We also added a new script to the FIRE distribution, that checks FIRE input
  files to make sure they are exactly in the right format. Usage is:

  perl TOOLS/FIRE_analyse_input_files.pl -expfile FILE1 -species TXT [ or -fastafile FILE2 ]

  where FILE1 would be an expression file. -fastafile FILE2 is used when you
  provide your own fasta file (FILE2). See tutorial for more information.


Nov 27, 2007: fixed a portability issue with the random number generator. We
  had to adopt a new, slightly slower but more portable random number
  generator. We also modified mi_combine to look for motifs that co-localize with
  themselves (to detect motif "clusters"). This would be shown by '+' signs in the diagonal 
  in motif interaction maps. 

  These are significant changes, so we made a new release, FIRE v1.1.
 
  FIRE v1.0 is still available for download and fully supported. Since motif
  optimization and statistical testing relies on random numbers, results obtained
  with v1.1 may sometimes be slightly different from those obtained with v1.0
  (equivalent to using a different seed for the random number generator).
  We stress that v1.1 results won't be better (or worse) than v1.0 results. 
  The only real difference is that v1.1 is less likely to crash when you run it.  
  
  Many thanks to Yeon-Ki Kim (GreenGene Biotech, Korea), Haitao Cui (National
  Institute of Biological Sciences, Beijing, China), and especially to
  Chanchal Kumar (MPI Munich) for reporting the issue and helping with the
  debugging. 


Nov 21, 2007: fixed a Segmentation Fault bug in mi_find, that was affecting an AMD 2-CPU (Opteron), 
  running FreeBSD 5.4. We traced the bug to the realloc() function, which we removed from the code. 
  Many thanks to Eli Stahl (UMass Dartmouth) for reporting the bug and helping with the debugging.

  
Nov 9, 2007: fixed a Bus Error bug in mi_optimize, that was affecting a Macbook running 10.4. 
  The bug was due to the pcre-6.4 library we were using. We know use pcre-7.4.
  Please re-download the FIRE.zip archive if you encounter this bug.
  Many thanks to Devin Scannell (Lawrence Berkeley Labs) for reporting this problem and 
  helping with the debugging.