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Pedigree drawing software

February 13th, 2007 by Mark · 2 Comments

Pedigrees are essential when documenting large complex families with inherited disease. I spend a lot of time looking after families with a variety of inherited neurological disease, and have spent a similar amount of time trying to find decent software to make this work easier!

I last did a systematic search for software last year. On Mac OS X, there appeared to be very little available, and what can be found is often not suitable for complex human relationships. For example, Pedigree/Draw cannot really cope with multiple marriages without having duplicate individuals, and even though it is now commercial software, has not been updated for a very long time.

To get things done, I’ve been using a Windows-based machine with Cyrillic. This is a commercial offering, and whilst clunky, is quite powerful. However, using it in practice is difficult – I sometimes wish to generate pedigrees with patient identifiable information (for use in medical notes) but more often than not, need to generate anonymous files. Getting the finished pedigree into PDF format for inclusion into a LaTeX document is laborious, and involves creating a PDF printer, checking all the printer settings manually, making sure the pedigree display settings are updated, and then finally transferring the PDF over to my main work machine (Mac). It is a pain, and makes making small updates inefficient: the pedigrees then become out of date as I don’t update them. I’ve also had problems with output quality, with some lines extending inside boxes or circles – not good for publication. This approaches means that generated pedigrees are often widely disparate in size and look odd when put together on a page.

Pedigree drawing is actually quite complex. Naive algorithmic approaches work in simple nuclear families, but researchers often map complex families, with consanguinity and multiple marriages. Many researchers also need to include phenotype and genotype data, and need to be able to generate data files for use in linkage analysis software. Researchers need to be able to generate attractive looking, standard-appearance pedigrees to publication-quality standard for inclusion in papers and theses.

Pedigree-drawing with R and graphviz

R is my current favourite working environment. I use it for complex data analysis, extracting data dynamically from multiple SQL-based databases, performing complex manipulation or aggregation and then generating publication quality tables and graphs.

This paper helpfully suggests two separate R packages that can be used to draw pedigrees. I have tried them both, and while good for simple families, I need a more comprehensive solution. For example, individuals can be marked affected or unaffected, but there is no built-in facility for marking individuals as “Unknown” with the standard approach of putting a question-mark within the circle or square. It is possible to annotate the plots with judicious use of R graphics primitives and adjusting the labelling system, but this is error-prone and there is no built-in facility for making sure lines do not cross text.

Pelican
This is a java based pedigree drawing program that can generate very simple pedigrees. It is a free download, and if your needs are not great, it may be sufficient. There is more information available in a formal bioinformatics article.

Madeline

I did not find Madeline until very recently. It is a mature and sophisticated pedigree management and drawing program available for all common operating systems, including Mac OS X, Windows and Linux.

Installation on Mac OS X:

  1. Download the software from their site. The current stable version is 0.935, but a version 2 series is also currently in development and worth evaluating.
  2. Unpack the tar.gz file. You can do this by double clicking in Finder, or using tar from the command line.
  3. Run:

    ./configure
    make
    sudo make install

    It requires an installation of GNU Readline 4. It will offer to download and install this automatically. I have tried to use my already installed readline (V4+5) libraries from macports, but did not manage to get this to work. Instead follow the instructions on http://eyegene.ophthy.med.umich.edu/madeline-0.935/compiling.html. I also had a problem with the make install step (“make: `install’ is up to date.”), and instead ran cd src; sudo make install which then worked perfectly.
  4. I will post some example pedigrees in due course.

Tags: Medical · Open Source · Research · Software

2 responses so far ↓

  • 1 Stacey // Nov 18, 2008 at 6:00 pm

    Have you come any further with Madeline yet? I am thinking of using it, but am new to the world of Mac…

  • 2 Stefania // Oct 10, 2009 at 2:08 pm

    Have you tried Haplopainter? It’s an opensource software to draw pedigree with Windows. It seems nice…

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