Looking for the Perfect Pedigree Software

Long ago, when our blog was young (less than 2 months old – where does the time go?), Mary wrote a post about the pedigree drawing programs that she knew of, or that were mentioned on the Mouse Genome Informatics (MGI) mailing list. There has been so much interest in that post, as judged by clicks, that we began looking into pedigree analysis tools with the idea of creating one of our trainings on the ‘best’ tool we found. I have been working on finding a great tool to train on – public (free), broad applicability and web-based. I did find a nice little tool named PediDraw, and did a tip of the week on that, but it is so easy to use it doesn’t really warrant a full tutorial.

But all in all, I’m finding the search to be a somewhat difficult slog. So much of the software I have found is fairly old, many of which are no longer supported by their creators. Others are only available commercially and/or have a very focused functionality, are only available on one system or the other, or are in various languages such as Fortran 77 or R. Last week I noticed that Mary’s blog was linked to in a blog post by Gregor Gorjanc, and I must confess that it felt great to know that he was having a similar slog for the ‘right’ pedigree program. Gregor’s post has some nice background information and information on for plotting large, complex animal breeding animal pedigrees. I won’t repeat his information here but his post, as well as others he links to, convinced me I should share some of the gems of knowledge that I have acquired.

The first thing I learned is how easy it was to find useless information (at least to me) by googling for ‘pedigree’ – as in almost 23 million hits with the top I-don’t-know-how-many linking to information or coupons for Pedigree dog food. As I searched, I also learned how many different things people mean by pedigrees – there are pedigrees for keeping track of livestock breeding programs, laboratory mouse strains, dog breeds, and fancy bird crosses. thoroughbred, others are for historians or hobbyists tracing their roots. The term pedigree is also used for business tracking and management software systems. The area that is closest to my personal interests are those that are medically relevant, but even those are amazingly diverse – pedigree can mean everything from a family history given by a patient (riskApps) to e-pedigrees soon to be required by some states for pharmaceutical manufacturers to reduce the chances of dangerous counterfeit chemicals.

Once I got a few promising hits, found some promising sites I tried to extend my searches using the words that were on the sites that I had found. Using search terms such as ‘kinfolk’ and ‘ancestry’ lead me to Anabaptist family databases and presidential genealogies, but not so many drawing programs. The most fruitful/directed search phrase was of course ‘pedigree drawing software’ which retrieved many articles and individual software pages. However, I think THE BEST hit (by far) that I found was the linkage software list at Rockefeller University, and I found it with the search phrase ‘linkage analysis software’. Why do I consider this THE best hit, you ask? Though my searches I have come to believe that pedigree drawing software is somewhat like religion – it is a very personalized thing & only you can know which is best for you. The Rockefeller list is the largest and most comprehensive list that I have anywhere. It is up-to-date and publicly available. It lists over 450 programs in an alphabetized list and provides information such as system availability, recent publications, brief description for each. There is also a searchable version of the list. If I were hunting for the perfect pedigree drawing program for my research, I would search here rather than Google! My hat is off to those who maintain this wonderful list at the Laboratory of Statistical Genetics at Rockefeller University!!

I’ll keep you posted as to my finds as I cull their list. And if you are ‘in the know’, or have found the ‘perfect’ pedigree software PLEASE do comment and add your knowledge here.

9 thoughts on “Looking for the Perfect Pedigree Software

  1. Jon Frost

    I have been searching the last few days as well for our in-house pedigree application which I have written. I’ll let you know if I find something. I really like the interface that these programs provide:
    http://www.mind42.com/pub/mindmap?mid=a6e2c232-a923-4fc9-9fb5-07bf6105e2a7
    http://live.yworks.com/yfiles-ajax/Examples/Collapsible_Tree.html

    But a good visualization tool that can be connected to our in-house database is proving very hard to find. thanks and all the best.

  2. Jennifer

    Hi Malcom,

    Thanks for the heads-up. We do know and appreciate Madeline! It is a lovely resource that has both web and download versions, good documentation and good functionality. We were considering creating a tutorial on it, but our scientist found that it wasn’t fully functional on his Mac. When he either used the scroll bar, or adjusted the size of the pedigree by dragging its window, the pedigree became ‘jumpy’ and difficult to view, or take screen captures of due to broken lines.

    Of course, our difficulty with screen captures in no way detracts from Madeline as a resource for pedigree analysis. And we may eventually try again with Madeline because it is so nice, but for now we are going to continue our search a bit more.

    Again, thanks for the heads up on Madeline! Feel free to keep us posted on any updates/news about the resource.

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  4. Jennifer Post author

    Thanks, Joost, for pointing out this commercial, multi-user application for plant breeding companies.

    Keep the resources rolling in to us!

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