History
New Features from 0.999 to 1.0
- Includes a comparative mapping method exploiting biological datasets and the knowledge of a completely sequenced genome having known orthologous relationships with some of the markers in the genome of interest. See "dsbplambda" or "pareto*" commands in the documentation. For that, a reference order dataset must be defined and merged ("dsmergor") with the biological datasets. The comparative mapping method uses a Bayesian model based on multipoint maximum likelihood and the number of breakpoints between a map and the reference order. Graphical views of the comparative mapping selection process and a comparison between a map and the reference order are also available.
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.
- 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:
- 0 = build framework and don't test remaining
markers.
- 1 = build framework and test all remaining markers
at each position of framework.
- 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 .
- 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.
- 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).
Last modified: Wed Oct 6 09:00:08 CEST 2004