WebLogo Release Notes WebLogo Release Notes 3.2 (2012-01-30) [Gavin Crooks, David Sivak] * Graphical interface now accepts transfac format motif files. * New output format option: SVG (Scalable Vector Graphics) * Miscellaneous minor bug fixes and refactoring. 3.1 (2011-08-16) [Gavin Crooks, David Sivak] Mostly bug fixes, code improvements and minor user enhancements. * Command line: Add parsing of transfac PWM files * Command line: Add reverse and complement transformations * Improve clustal file parsing * Currently compatible with python 2.5, 2.6 and 2.7 * Deprecate support for python 2.3 and 2.4 * Migrate corebio library into weblogo for easier maintenance and development. * Add new annotate option for custom annotation line * Miscellaneous minor bug fixes and refactoring. * Incorporates bug fixes and feedback from Gavin Crooks, John Gilman, Kevin Schutz and Perry Evan. 3.0 (2008-10-14) [GEC] A significant update of WebLogo. New and improved feature include: * Simplified GUI. More useful options, less obscure options that are rarely used. * Several choices of unit including bits and nats, and corresponding energy measures such as kJ/mol. * Error bars are smaller and more discrete. * The size of logo stacks is consistent (Does not change with sequence length.) * The width of the characters in a stack are scaled by the fraction of non-gaps. Therefore gappy columns are visually less important than columns with gaps. * Three standard logo sizes. * Can now read many multiple sequence alignment formats, including CLUSTALW, FASTA, plain flatfile, MSF, NBRF, PIR, NEXUS and PHYLIP. * High resolution PNG output. * New, rational, easy to use command line client. * Python based API library. * New color schemes, including Watson-Crick pairing, hydrophobicity and charge. * I (Isolucine) now shows crossbars, so that the letter is distinguishable from a line. * Colors can be specified using CSS2 syntax. * Optional figure label. * Conservation is now calculated as the Bayesian posterior mean relative entropy. (This is the most significant change scientifically. The math needed to get this right is very interesting.) * Similarly, we now display Bayesian 95% confidence intervals for error bars. * Compositional adjustment. * Includes contributions from Clare Gollnick, David Ding, John Gilman. * Incorporates bug fixes and feedback from John Reid, Gordon Robertson, Eric Odell, Krisztina Gabor, ... * Incorporates or adapts ideas and code from Gary Hon, Steven Brenner, John-Marc Chandonia, Liana Lareau, Ed Green, James Casbon, Jeffrey Chang, Frank Kauff, Cymon J. Cox, ... ----------------------------------------------------------------------- 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 WebLogo change log ----------------------- + New feature * Changed/Improved feature ! Fixed bug - Removed feature Versions : major.minor.patch. The WebLogo Team ------------------ LL: Liana Lareau GEC: Gavin E. Crooks GH: Gary Hon JMC: John-Marc Chandonia SEB: Steven E. Brenner