Introduction
Drawing pedigrees by hand is exhausting and time-consuming. That’s one reason why software like HaploPainter is being developed. It fact to date there is no software that meets the demands of all users. Why is that so? First of all, drawing pedigrees automatically from family describing flat files is not easy – i think that every programmer would agree with me at this point. The difficulties for finding a cross free or minimized and human nice looking drawing solution in a moderate time are enormous! Second, the development of pedigree drawing software is mostly motivated to fit into a primary target audience such as genealogists, genetic counselors, scientists or breeders, and all of them have other feature requests. HaploPainter is basically aimed at bioinformation scientists and genetic counselors.
One challange of the last time was and is the integration of very long haplotypes (they describe the inheritance of chromosomes). Haplotypes are products of linkage analysis – formerly often based on a couple of polymorphic microsatellite (STR) markers. If you do not belong to the category genetic counselor or bioinformatics you probably don’t know from what I speak. In that case feel free to think of HaploPainter as a common pedigree drawing software. For all others: you probably were not really satisfied with the ability of existing software to draw nice looking pedigrees together with nice looking haplotypes - especially when you dealt with SNP's derived from whole genome scans.
HaploPainter’s main concern was and is to overcome this situation and to provide an applicable and simple to use solution for drawing pedigrees with long haplotypes. As linkage proven scientist you can think of HaploPainter as a tool to combine pedigree data with haplotype and mapping data to produce high quality graphics ready for publish. Typically you would point to Mendelian diseases in terms of reliable definition of the smallest critical interval harboring the underlying gene defect.
Features
- Import of pedigree data from common linkage format, HaploPainter format or MySQL, PostgreSQL or Oracle data tables
- Support Unicode encoded pedigree files
- Import of haplotype data from Merlin, Simwalk2, Genehunter and Allegro
- Symbol nomenclature based on the Pedigree Standardization Task Force
- Full drag and drop for symbols
- Manually and automatic selection of loop breaking
- Export high quality graphic to SVG, Postscript, PDF, PNG
- Plenty of drawing style features
- Command line mode for creating graphics in a shell environment
- Modify your pedigree within the graphical user interface
- Written platform independent in Perl
Citation
Holger Thiele and Peter Nürnberg (2004) HaploPainter: a tool for drawing pedigrees with complex
haplotypes Bioinformatics. 2005 Apr 15;21(8):1730-2. Epub 2004 Sep 17.
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Contact
Email to the developer