

WebLogo Version 2.8 


  Gavin E. Crooks, Gary Hon, John-Marc Chandonia and Steven E. Brenner 
    Genome Research, 14:1188-1190, (2004) 


Release Notes:
  (Known bugs that can't be quickly fixed are listed below.)

  2.8.2 (2005-09-08)  [LL, GEC]
      Various Bug fixes:
        * Fixed Yellow (Was orange)
        * Various improvements in handling malformed input.
        * Fixed the fineprint checkbox option, which was stuck on.
        * Renamed "Uniform Height Logo" option to a more descriptive
          "Frequency Plot", and removed deceptive y-axis.

  2.8.1 (2004-10-18) (Minor bug fix release) [GEC]

    Bug fixes:
     * Made weblogo compatibly with ghostscript version 8.1x.
        This release is known to work with ghostscript version 7.05, 8.00 & 8.14

    Kudos for bug reports and suggestions to:
     * Lei Shen   


  2.8 (2004-10-01) [GEC]

    Bug fixes:
     * Fixed another form data parsing bug whose only apparent effect was to
        fill up the webserver's error log.
     * Fixed an issue with using double slashes in weblogo's url.
 
    Kudos for bug reports and suggestions to:
     * Eric Odell    
     * Scot Wolfe
     * Alban Mancheron
     * Ed Green

     
  2.7 (2004-06-09)  [GEC]

    Bug fixes :
     * Fixed logo.cgi's parsing of checkbox form data.
     
    Kudos for bug reports and suggestions to:
     * Eric Odell


  2.6 (2004-03-15)  [GEC, GH]

    Bug fixes:
     * Resolved an issue with hard coded paths within the 
        seqlogo command line client
     * Improved the parsing of clustalw files

    Kudos for bug reports and suggestions to:
     * Allen Liu
     * Guo Anyaun
     * Harald Weber


  2.5 (2004-02-19)  [GEC, GH]

    New features and enhancements :
     * Added multiline logos.


  2.4 (2004-01-29) [GEC, GH]

    New features and enhancements :
     * Added file upload for sequence data.
     * Updated main page to reflect updated publication status


  2.3 (2003-11-03) [GEC, GH]

   New features and enhancements
     * Added ability to parse CLUSTALW and flat file multiple sequence
       alignment formats.

    Bug fixes:
     * Antialiasing PNGs now works with recent versions of ghostscript
     * Can now change output file type when using Mozilla.

 
    Kudos for bug reports and suggestions to:
     * Stefanie Lager
     * Ed Green
     * Michael Galperin 


  2.2 (2003-08-01) [GEC, GH]

    Several minor bug fixes and changes to the web pages.
     * Fixed various buggy command line options
     * A request for an empty yaxis label is now respected
     * Fixed a major bug in temporary file name assignment
       that prevented weblogo from running on some unix variants

    New features and enhancements 
     * Made error bars darker
     * Added option to control distance between tic marks
 
    Kudos for bug reports and suggestions to
     * Stefanie Lager
     * Arlin Stoltzfus
     * JP Cartailler  
     * Peter G. Warren
    

  2.1 (2003-01-08) [GEC]
    
    Several minor bug fixes and changes to the web pages.

  2.0 (2002) [GEC, GH, JMC, SEB]

    This second version of WebLogo is a complete rewrite of both
    the user interface and the backend. Many new features and
    options have been provided.

  1.0 (1995) [SEB]

    The original version of WebLogo was written in 1995 by Steven 
    Brenner, and was hosted by the School of Biological Science, 
    University of Cambridge




Installation

  After unpacking the tarfile, it should be possible to immediately create
  logos using the seqlogo command line client.

      ./seqlogo -f globin.fasta > globin.eps   

  WebLogo requires a recent version of gs (ghostscript) 
  <http://www.cs.wisc.edu/~ghost/> to create PNG and PDF output, and 
  ImageMagic's convert <http://www.imagemagick.org/> to create GIFs.

      ./seqlogo -F PDF -f globin.fasta > globin.pdf   
      ./seqlogo -F PNG -f globin.fasta > globin.png
      ./seqlogo -F GIF -f globin.fasta > globin.png

  To use WebLogo as a web application, place the WebLogo directory
  somewhere within the document root of your webserver. Your webserver 
  must be able to execute logo.cgi (seqlogo is the command line interface,
  logo.cgi is the web interface) and read/write to the cache directory. 
  Copy the file logo.conf.init to logo.conf, and edit the paths found   
  within so that logo.cgi can find gs
  and convert.

  Apache: In the httpd.conf file, you may have to add an ExecCGI
  option to the weblogo directory, and add a cgi handler.
  Something like...

     <Directory "/home/httpd/weblogo/pub">
         Options FollowSymLinks MultiViews ExecCGI
         AllowOverride None
         Order allow,deny
         Allow from all
     </Directory>

     AddHandler cgi-script .cgi


Known Bugs:
  * Some installation problems can cause WebLogo to fail without returning
    any useful error message. Please double check the installation directions.

  * GIF and PNG logos cannot be saved correctly in IE for windows.
     The logos display correctly, but when you try to save them the only file 
     type option is BMP! One workaround is to copy the image url into another
     IE window and reload the image. IE will then allow you to save the file
     with the correct filetype. Other workarounds are to use a different web
     browser, or a different OS (Or both).
     
  *  The "I" charachers representing isoleucine residues aren't easily  
     identifiable as "I" charachers in the WebLogo font.

  *  The Outline Characters option turns off antialiasing.

  *  Frequency plots will not show the y-axis scale or label.
 
The WebLogo Team :

  LL:  Liana Lareau
  GEC: Gavin E. Crooks
  GH:  Gary Hon
  JMC: John-Marc Chandonia
  SEB: Steven E. Brenner 



 
 