Remarques sur les révisions

Nom de version : CarthaGène 0.999 and Active Tcl package(with the LKH code)

Notes

a research version which can only be used for non-commercial research purposes only (because it contains code with a specific restricting license). 

Windows installation

To install CarthaGene on Windows, you must do the following:

   1. uninstall any previous version installed. This means that you must both delete the previous CarthaGène directory and uninstall the Tcl/Tk package (from the windows Control Panel)
   2. unpack the carthagene0.99.exe archive you downloaded.
   3. in this directory, double click on the Active Tcl/Tk windows installation kit (file ActiveTcl8.4.2.0-win32-ix86.exe).
      WARNING, to install this package you must be a privileged user (Windows XP, 2000 or NT) or the rest of the installation will fail.
   4. Once Tcl is installed, double-click on the InstallWin Tcl file. This will create the tclshrc, cgwopt… files needed by CarthaGene
   5. This is it. You can directly execute CarthaGene by going in the gui directory and double-clicing on the CGW file.

      For ease of use, you can create a Shortcut to this file and put it in your favorite location (eg. Menubar).
   6. If the user interface doesn't start, check the contents of the cgwlog file for error messages.

If you don't want to use the graphical interface but only the Shell interface, simply launch TkCon (available in the main Windows application menu, under the ActiveTcl line) and load the tclshrc.tcl (File menu, Load File item). file from it. 

Journaux

New Features from 0.99 to 0.999

    * Integration of the LKH (Link-Kernighan) travelling salesman heuristics to speed up haploid/diploid RH mapping (non merged data). See commands "lkh*".
    * Obligate chromosome breaks in RH can now be computed and used as a criteria for lkh. See "lkhocb".
    * Ability to export RH data to TSPLIB format (eg. to use the Concorde package). See the "cg2tsp" command.
    * Ability to export maps to XML format. This XML format for maps is also read by the companion softwares: GENOPLANTE ® MCQTL software for QTL-mapping in multiple populations and GENOPLANTE ® BioMercator software for the meta-analysis of QTL detected in independent experiments. These tools are available from Génoplante web site .
    * Two-points matrix is now printed correctly for RIL pedigree. Several minor bug corrections and valgrind'ed code.

New Features from 0.5 to 0.99

    * A new command "heaprinto" is available. It enables to compare the positions of the loci of all the maps into the heap.
    * A new command "maprintdr" is available. It enables to print a map in details in the reverse order.
    * The heaprint command is enhanced. A new column displays the cumulative distances. The pos column displays the absolute position of the locus on the map.
    * The mrkfr2p command applies to the current selection of loci only.
    * The MrkTest flag of the buildfw command now accept 3 values:
          o 0 = build framework and don't test remaining markers.
          o 1 = build framework and test all remaining markers at each position of framework.
          o 2 = the framework is given in {}, then all the markers in the selection are tested at each position in the framework.
    * The heaprintds/heaprints commands are removed. They are available as heaprintd/heaprint respectively.
    * The Buildfw command is available as a button, with corresponding options.
    * Markers with compatible information can be detected using the mrkdouble command and merged together using the mrkmerge command.
    * It is now possible to change the level of convergence of the EM algorithm using the cgtolerance command. The maps in the heap are reestimated using the new level.
    * A Detailed option is available in Maps menu to print the best m ap with 3 parameters to customize display of map.
    * A user documentation is available
    * The license key is removed. CarthaGene goes under GPL/Q licenses.
    * The cgout command allows to save carthagene output in a file.
    * The mrkmerget command allows to get the list of merged markers
    * The cgsave command allows to save a working context.
    * New commands to map list of numerical Ids to lists of names and vice-versa are available. See mrknames and mrkids.
    * New commands to directly print the best map know are available (bestprint and bestprintd).
    * the greedy command (tabou search) can be used to perform only a single (or few) best submap inversion (2-CHANGE). This is done by giving greedy a negative amount of extra iterations.
    * New commands to computes an intuitively nice marker ordering using 2-points information (mfmapd and mfmapl). They are faster than nicemapd and nicemapl and can provide better results.
    * when merging 2 datasets by order, two different orders may be easily shown to be obviously equivalent (same loglikelihood). These equivalent orders may completely saturate the heap. The heapequiset command is available to only insert in the heap maps with no equivalent orders in the heap.
    * new commands (cgrobustness/cgnorobust) to stop the search when the difference between the loglikelihood of the best map and the loglikelihood of the second best map is lower than a given threshold. It can speed up the validation process of a framework map, for example when the greedy command is applied after the buildfw command.
    * the greedy command (tabou search) receives a new optional parameter in order to control its speed. Typical value is 25% (i.e. x4 faster). Of course, a small value will have an impact on the map quality .

New Features from 0.4 to 0.5

    * diploid RH data is now handled by CarthaGène.
    * A new command is available. "cgversion" returns the version of the software.
    * The command "group" now applies to the current selection of loci only.
    * Each time a new data set is loaded (dsload), the current selection of loci is automatically fixed to the set of all the loci of this new data set (except for constraints data sets).
    * A new command is available. "heaprinto" enable to compare the positions/orders of the loci of all the best maps found by Carthagene (stored into the heap).
    * A new command is available. "maprintdr" enable to print a map in details, using a reverse marker ordering.
    * The heaprint command has been enhanced. A new column displays the cumulative Haldane distances and the pos column displays the absolute position of the locus in the map.
    * The ``Distance threshold'' argument of the group command is now in Morgan (bug in earlier version).
    * Several bugs corrected.

New Features from 0.3 to 0.4

    * ctrl-c will interrupt a running command. The heap of already computed maps is available and consistent.
    * A new command is available. "buildfw" enable the user to build a framework map.
    * The "InitTemp" argument of the annealing command is now adaptative. The temperature can increase until a good threshold of accepted change is reached by the algorithm.
    * (gui) By using the "Carthagene Locus Selection" Dialog, you can specify any order of loci you want to test.
    * (gui) A new button "Stop" is available. It enables the user to interrupt a running command. The heap of already computed maps is available and consistent.
    * (gui) A new button "Defalgo" is available. It enables to run a default set of commands. By editing the  /.cgwdefalo, you can specify your own automated process (using the tcl language).
    * (gui) The log file .cgwlog is now located in /tmp and has a session id (ex: /tmp/.cgwlog134).
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