[02/11/2009] Marine Dumousseau (marine@ebi.ac.uk) Changed the MELTING 5 documentations (references and acknoledgement) Changed the files in the testResults folder. [23/10/2009] Marine Dumousseau (marine@ebi.ac.uk) Fixed some bugs in the inosine and single mismatch files. Added other tests. Changed the JAR File. Fixed a bug for the hydroxyadenine model. Put by 'all97' as default DNA Crick's pair thermodynamic model version 5.0.2 [14/10/2009] Marine Dumousseau (marine@ebi.ac.uk) Fixed some bugs in the melting.bib file. version 5.0.1 [08/10/09] Marine Dumousseau (marine@ebi.ac.uk) Fixed some bugs in the Javadoc. Created a build.xml file and buildProject.sh to build the project. [28/08/09] Marine Dumousseau (marine@ebi.ac.uk) Fixed a bug for the option -O in OptionManagement. Created the CompatibleMain class which allow a compatibility between MELTING 4 and MELTING 5 options (except for the option '-q'). [17/08/09] Marine Dumousseau (marine@ebi.ac.uk) Version 5 in Java. New thermodynamic models and parameters for : Crick's pair, single mismatch, tandem mismatch, internal loop, single dangling end, double dangling end, long dangling end (only poly A), inosine, hydroxyadenine, azobenzene, locked nucleic acids, single bulge loop, long bulge loop. New corrections for sodium, magnesium or mixed Na, Mg. New corrections for DMSO and formamide. [01/JUN/2009] Marine Dumousseau (marine@ebi.ac.uk) tkmelting.1, tkmelting.1.xml and melting-gui.desktop added. acknoledgements updated in the different documentation files. version 4.3b [15/APR/2009] Marine Dumousseau (marine@ebi.ac.uk) mac executable added. [14/APR/2009] Marine Dumousseau (marine@ebi.ac.uk) Index.html added to the DOC folder. linux 64 bits executable added. [03/APR/2009] Marine Dumousseau (marine@ebi.ac.uk) Documentation modified. [31/MAR/2009] Marine Dumousseau (marine@ebi.ac.uk) mistakes in the thermodynamic tables corrected. Documentation modification. [31/MAR/2009] Marine Dumousseau (marine@ebi.ac.uk) inosine parameters added [30/MAR/2009] Marine Dumousseau (marine@ebi.ac.uk) Perl interface bugs correction and move some files. Calcul.c and melting.c bugs correction. [27/MAR/2009] Marine Dumousseau (marine@ebi.ac.uk) Correction of the function which computes the fraction of GC base pairs. We can now take in account the mismatches CXor GX and inosine mismatches IG or IC. New parameters of Santalucia added [26/MAR/2009] Marine Dumousseau (marine@ebi.ac.uk) add the inosine parameters. (from Santalucia 2005 for DNA duplexes and from Brent M. Znosko 2007 for RNA duplexes (only IU base pairs)). add the option -i for enter a new set of inosine parameters. version 4.3 [25/MAR/2009] Marine Dumousseau (marine@ebi.ac.uk) add the magnesium correction. (algorithm from Owczarzy 2008, only for DNA/DNA duplexes) add the options -k, -t, -G for the potassium, tris and magnesium concentration. The Tris+ concentration is about the half of total Tris concentration. version 4.3 [24/MAR/2009] Marine Dumousseau (marine@ebi.ac.uk) Fix mistakes in the calorimetric table sug95a.nn. version 4.2i [08/AUG/2007] Nicolas Le Novère (lenov@ebi.ac.uk) Move from isolatin-1 to utf-8 version 4.2h [06/SEP/2004] Nicolas Le Novère (lenov@ebi.ac.uk) Fix mistakes in the calorimetric table xia98a.nn. version 4.2g [20/MAY/2004] Nicolas Le Novère (lenov@ebi.ac.uk) Fix a mistake in the calorimetric table xia98a.nn. Thanks to Wong Chee Hong (wongch@bii.a-star.edu.sg) version 4.2f [10/APR/2003] Nicolas Le Novère (lenov@pasteur.fr) Minor modification of the verbose output. version 4.2e [11/FEB/2003] Nicolas Le Novère (lenov@pasteur.fr) Modification of the documentation, regarding the correction of strand concentration. version 4.2d [03/OCT/2002] Nicolas Le Novère (lenov@pasteur.fr) Bug fix: An amazingly obvious mistake was introduced in the approximate mode. The fractional GC was used instead of the percent GC (Personnal view: The approximate mode is a crap anyway). version 4.2c [14/MAY/2002] Nicolas Le Novère (lenov@pasteur.fr) Bug fix: a break was forgotten in the big switch decoding the options. Also the output of long messages did not comply with ISO restrictions on string length. I split the strings. Thanks to Mauro Petrillo. version 4.2b [18/FEB/2002] Nicolas Le Novère (lenov@pasteur.fr) The threshold between exact and approximative computation is now controlled by an option. version 4.2 [14/FEB/2002] Nicolas Le Novère (lenov@pasteur.fr) Correction of a typo in all97a.nn An entropic factor was changed from -22.5 to -22.7 cal.M-1.K-1 version 4.1h [19/NOV/2001] Nicolas Le Novère (lenov@pasteur.fr) Corrections of the script profil.pl version 4.1g [18/MAY/2001] Nicolas Le Novère (nl223@cus.cam.ac.uk) Typographical mistake in decode.c:read_mm() If the environment variable was undefined, or there was no readable file at the specified place, the default defined at compilation was not read. Several minor editing of the error messages. Modification of the Tk interface. version 4.1f [03/MAY/2001] Nicolas Le Novère (nl223@cus.cam.ac.uk) Big mistake in documentation (relative to the correction of nucleic acid concentration). Took advantage to improve the documentation (including benchmark results). Minor correction of usage function. version 4.1e [29/APR/2001] Nicolas Le Novère (nl223@cus.cam.ac.uk) No need to enter a useless concentration of nucleic acid when using the approximative mode. Small (but important) edit of the script multi.pl. Addition of a benchmark in the directory TEST, which compare various methods, NN sets, and salt corrections. version 4.1d [20/APR/2001] Nicolas Le Novère (nl223@cus.cam.ac.uk) Correction of several critical bugs in the reading of paramaeters for mismatches and dangling ends. The format of the file containing the parameters for mismatches is modified (the undetermined Crick's pair were previously commented out. They are now included with parameters equal to 99999). version 4.1c [10/APR/2001] Nicolas Le Novère (nl223@cus.cam.ac.uk) Correction of the code to prepare the implementation of dnarna and rnarna mismatches and dangling ends. Correction of the makefile for unices version 4.1b [29/MAR/2001] Nicolas Le Novère (nl223@cus.cam.ac.uk) Implementation of the dangling ends analysis. Addition of a several security corrections (strcpy -> strncpy, check of malloc success ...). Improvement of the makefile for Unices. Simplification of the declaration of PATH for the nnfiles. [07/AUG/2000] Nicolas Le Novère (nl223@cus.cam.ac.uk) version 4f. Mistakes in the NN file san96a.nn found by Leo Schalkwyk (l.schalkwyk@iop.kcl.ac.uk) [05/JUN/2000] Nicolas Le Novère (nl223@cus.cam.ac.uk) version 4e. Correction of the output to stderr et stdout (number of spaces leading the lines). New perlTk interface. [26/APR/2000] Nicolas Le Novère (nl223@cus.cam.ac.uk) version 4d. Typos in the code and the perl/Tk interface (unit of entropy was given as J.Mol-1 instead J.Mol-1.K-1) [24/APR/2000] Nicolas Le Novère (nl223@cus.cam.ac.uk) version 4c. Addition of a script (profil.pl) allowing an iterative computation along a sequence, by sliding a window of a specified width. Minor modifications of the documentation. [09/FEB/2000] Nicolas Le Novère (nl223@cus.cam.ac.uk) version 4b. Some fixes of the program output and of the documentation. Handle of the references in the parameter files modified. [08/FEB/2000] Nicolas Le Novère (nl223@cus.cam.ac.uk) MELTING4 release version. Corrections on the advice of Nicolas Joly. Improved documentation. [05/FEB/2000] Nicolas Le Novère (nl223@cus.cam.ac.uk) Changed the behaviour of options -v and -q. Improved documentation. [29/JAN/2000] Nicolas Le Novère (nl223@cus.cam.ac.uk) Fixed bugs in the interactive mode. Improved online help (option -h). Fixed a lot of bugs or unpleasant features in the option parsing. Changed the behaviour of options -A and -H. The former has now always precedence over the latter regarding the et of NN parameters. [27/JAN/2000] Nicolas Le Novère (nl223@cus.cam.ac.uk) Second beta version. Correction of some NN files. Modifications of documentation. [26/JAN/2000] Nicolas Le Novère (nl223@cus.cam.ac.uk) First beta version. The program can now take in account mismatched hybridisations. Correction of a bug in the screening of Crick'pair. [24/JAN/2000] Nicolas Le Novère (nl223@cus.cam.ac.uk) alpha5. The program can now read a file containing the nearest-neighbor parameters for some mismatched Crick's pairs. [18/JAN/2000] Nicolas Le Novère (nl223@cus.cam.ac.uk) on suggestion of Nicolas Joly (njoly@pasteur.fr) alpha3 and alpha4. Code correction only. [17/JAN/2000] Nicolas Le Novère (nl223@cus.cam.ac.uk) alpha2. Modified the system to localize files containing set of nn parameters. Now a directory is defined at compilation by preprocessor directive. However, an environment variable can be defined, which targets a directory where to find a nn file. If it was not found there, it will be searched in the default directory. Therefore, a user can define its own set of parameters, while still using those installed with melting.