HapStar: automated haplotype network layout and visualization


  • A. G. F. TEACHER,

    1. Department of Biological Sciences, Royal Holloway University of London, Egham Hill, Egham, Surrey TW20 0EX, UK
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    •  Current address: Ecological Genetics Research Unit, Department of Biosciences, P.O. Box 65, FI-00014 University of Helsinki, Finland.


    1. FoAM vzw, Koolmijnenkaai 30–34, 1080 Brussels, Belgium
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A. Teacher, Fax: +358-9-19157694; E-mail: amber.teacher@helsinki.fi


Haplotype networks are commonly used for representing associations between sequences, yet there is currently no straightforward way to create optimal layouts. Automated optimal layouts are particularly useful not only because of the time-saving element but also because they avoid both human error and human-induced biases in the presentation of figures. HapStar directly uses the network connection output data generated from Arlequin (or a simple user-generated input file) and uses a force-directed algorithm to automatically lay out the network for easy visualization. In addition, this program is able to use the alternative connections generated by Arlequin to create a minimum spanning tree. HapStar provides a straightforward user-friendly interface, and publication-ready figures can be exported simply. HapStar is freely available (under a GPLv3 licence) for download for MacOSX, UNIX and Windows, at http://fo.am/hapstar.