Latest update: december 2007

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GGT, what is it ? Click to find out more.. 

GGT Updates :

 

update Sept 2007

• Move of genetic distance section to main selection form

• Several bug fixes

 

update Feb/March 2007

• Fixed a small bug in calculation of genetic distances using allele sharing for multi-allelic markertypes

• Addition of option to save pair-wise genetic distances to a text file (in addition to excel, MEGA and NEXUS)

• Fixed a small bug on opening compound data file with comments

• Added option to 'fix' genotypes when using optimized subset selection. Fixed genotypes are forced into the selected subset.

• Filename remains visible in the GGT title area

• Modified GGT 2 program icon

• Additions and explanations in manual

 

update Jan 2007

• Renamed GGT to GGT 2.0 to reflect the added functionality in the program name

• several small bug fixes

• option to transpose trait datasheet

• option to save and reload current selection of genotypes to separate, small text file (useful for subset selection results etc)

 

update Dec 2006

• Revision of the MANUAL, many previously poorly documented features were added

• Addition of a routine to perform SUBSET selection, iteratively searching for subsets that maximize the remaining diversity

• Alternative layout of import of spreadsheet formatted data. markers that contain in the same row in adjacent cells: name, chrom-no, map pos, alleles are now supported

• added to install package: small example excel files to demonstrate import and recode

• fixed a bug in the GGT-build option for loc files with comments (preceded by ';')

 

 

update Nov 2006

 

• Drag and drop .GGT files to the program window to open files
• LD calculations not limited anymore to within chromosome calculations + speed improvement
• LD Heat plot added
• Spreadsheet interface add row/column option added to allow entering of large datasets in parts by copy/paste
• Bug fixes related to selection of genotypes and traits
• Trait histogram bug fixed
• Manual updated

 

 

update Sept 2006

maintenance update.

• More bugs in calculations fixed (division by zero errors trapped)
• Interface simplifications and graphical updates
• More detailed marker statistics
• First beta option for association analysis using multi-allellic markers (eg SSR/SNP)

 

update Mar 2006

The 2006 version of GGT is here. Newly introduced bugs were mostly fixed in this edition. Features were further extended and also the manual was updated.

New options are:

• 3D look bar drawing
• small bugs in LD calculations fixed, new LD measurement options added
• Trait data distribution plots
• Whole genome Association plots/heatmaps
• Direct neighbor joining and UPGMA clustering from within GGT (external treeviewer needed to open Newick style tree files)
• Re-arrange settings page for better overview
• label drawing/ ggt file saving bugfixes...
• Manual updated, index page added

 

update Jan 2006

a new version of GGT is underway. It will be announced in a computer demonstration session at PAG2006 (abstract), a beta version of GGT2006 is now available from this website. This version is fully functional but still lacks a few example data files and the manual is not yet complete.

New options are:

• Import from spreadsheet, with on-the-fly recoding of complex allele data
• Filtering & selection of genotypes based on marker criteria
• Calculation of inter marker LD
• Calculation of genetic distances and marker-trait associations
• Sorting of genotypes based on marker or trait-values
• a bunch of bugfixes...
   

update Apr 2005

- Fixed bug not displaying allele name in legend
- Improved 'build ggt file' option: 'alias' names are now allowed in loc file
- Fixed the auto-scaling of plots within the available drawing window
- Completely new module for 'view all' option displaying the entire genome for all individuals as horizontal lines
- Improved and extended print preview and print options, introducing multi-page print preview and prints!

 

update Mar 2005

- Fixed drawing bug in individual view
- Fixed group identification in legend text
- Improved 'build ggt file' option for CP population, now deals correctly with phase and segregation information
- Long filenames are accepted in 'build ggt file' option

 

update Jan 2005

- Improved marker label placement =>
- export to MEGA
- loci sorting bugfix
- added top margin option in settings
- added icons in main menu, replaced 'build ggt file' menu icon

 

update Oct 2004

- Added a new data type: QTL
- display QTL interval bars within GGT, also export to Mapchart
- click here to view an example input file containing the QTL type
- compare individuals in one image! (select up to 10 from indiv & selection tab and click compare button) [beta]
- bugfix: statistics Pie
- bugfix: start of chromosome at position 0 when actual first position was > 0

 

update Sept 2004

- Added options to use characters 0-z (74 options) as allele identifiers. So also 0-1 coded alleles should work!
- Added next group / prev group buttons to toolbar
- Added option to use hatch styles in color display. 8 styles available that together with custom definable colors should be plenty to make your markers stand out.
- statistics and cleanup bugs fixed
 

update Oct 2002

- Added Print Preview!  finally you can see what you print, with print scaling options.
- Specify selection with the keyboard (use CTRL while typing for reverse selection)
- Fixed bugs in selection display window
- Added sorting status to status bar

update June/July 2002

- Redesign of program interface, more drawing space created
- Added option for sorting data based on marker/ groups, aliases
- Export to new Mapchart 2.0 type
- informative status bar shows individual "under the mouse"
- many bugfixes and code cleanup
- many CP-population specific additions (phase estimation, selection) 
- New Nullsoft install system
- Allow whitespace in aliases (eg ALIAS "my variety 1" "parent 2"  etc..)
 

update Jan 2002

- data in single file
- Allow up to 26 alleles (A-Z)
- allow selection on marker ABSENCE
- many bugfixes and code cleanup

update Sept 2001

- Bug fixed that displayed wrong individuals when right-clicking and selection active
- More robust handling of import of map files. e.g. chom "mychrom 1" is now allowed 
 

update April 2001

-Bug fixed that clipped a saved EMF image to the size of the screen (finally..)
-Introduced option to skip markers that are too close to each other (avoid cluttering)
-Introduced option to remove legend, bottom-text, ruler etc from your drawing when desired
 

update February 2001

-Save and recall settings per project
-Draw everything in a single image
-Combined drawing for EMF, screen & prints
-Selection made easier, and results drawn without "gaps"
-Switch between selected view and complete view without clearing selection settings
-Change/Edit the raw data and instantly see the effect on the GGT image (i.e. when looking for mis-scorings, or marker-position swaps etc..) (figure below)
-More robust reading of data and building of GGT files from raw locus data
-Export of single individual maps, including colored regions to MapChart format
-New color selection box, allows selection of all possible colors from the windows palette (image below)
-Edit the raw data or marker position on the map [menu: edit]

- New color selection box and option to remove the cM ruler + save & recall settings at will

update October 2000

-Included a legend for genotype codes (A, B, H etc)
-New option to export GGT images to EMF (enhanced metfile Hi-Res) image format
-Better "build" (merge of map and locus files), GGT files now get meaningful names taken from chromosome title in map file
 

update August 2000

-fit bars to height
-New installer makes life easy and registers the .ggt filetype also for editing (try right clicking a GGT file)
-Printing routine enhanced
 

update May 2000 

CP module modified, various enhancements. One (right-)click selection of individuals from population drawing.
 

update May 1999 (32 bit version only):

Better printing of Black&White images, scalable length of chromosomes, data editing, JPEG support, Scale in cM printed.

 

Why GGT?

GGT stands for Graphical GenoTypes. A graphical representation of molecular marker data can be an important tool in the process of selection and evaluation of plant material. A computer program was developed that enables representation of molecular marker data by simple chromosome drawings in several ways. Commonly used marker file types that contain marker information serve as input for this program, which was named ‘GGT’. Besides representation, GGT can also be used for selection or filtering and much more!

• if this explanation is too brief, please consult the GGT manual

You may also want to have a look at the FAQ (frequently asked questions), containing answers to common problems and Tips and Hints

 

 

What does GGT look like ?

Here are some recent screenshots of GGT  "in action". Note that the "gradient drawing option" can be turned off! It is fancy but slows down performance quite a bit.

new layout: data unsorted	Focus on individual genotype	Multiallele display using hatch and color variations
after sorting:	Cross pollinated populations are also supported	QTL bars within GGT !
Compare genotypes in one image	the new 'show all' option

 

Availability

The GGT software is available through this site.

We ask you to leave your email in order to inform you on GGT updates.

Download GGT  2.0 - latest build (for date see last update remark on top of this page) (Windows 95/98/ME/2000/XP) version (self installing package: ~3 MB)

by downloading GGT I agree to acknowledge the software and its authors if I apply it in research that leads to a scientific paper.

*We will NOT use the submitted email address for anything else than informing you on GGT updates. We expect to release one or two updates yearly.

To do list:

• create a proper context sensitive help file
• improve genotype comparisons plots
• improve autosizing 'show all' drawing
• fix selection in CP populations
• your suggestion ?

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Please send comments, questions etc. to the webmaster page updated: december 2007  | Back to Plant breeding homepage

 

March 2007 overview of the origins of GGT users (note that all .com .edu  etc were arbitrarily attributed to USA)

 
 

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Disclaimer

The expertise group Plant Breeding is a cooperation between the Laboratory of Plant breeding of Wageningen UR and the business unit Biodiversity and breeding of Plant Research International.

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