fuzziness in MLG determination?
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david...@hutton.ac.uk
Jun 27, 2014, 8:02:10 AM6/27/14
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Dear Zhian
In examining populations of mixed ploidy P. infestans using 12 SSR markers we would like to automatically define clonal lineages. The MLG function looks useful but within our data there are isolates of the same 'clone' with very minor sub-clonal differences at say 1-3 loci. Unsuprisingly these cluster together in heatplots and Bruvo distance trees but the MLG function would not define them as the same MLG. Is there an option to define MLGs on the basis of Bruvo distance thresholds? For example 0.0 to 0.10? This would be nice function and I welcome your thoughts - if you or others have invented this wheel there is no need for us to do so again. Regards David
In examining populations of mixed ploidy P. infestans using 12 SSR markers we would like to automatically define clonal lineages. The MLG function looks useful but within our data there are isolates of the same 'clone' with very minor sub-clonal differences at say 1-3 loci. Unsuprisingly these cluster together in heatplots and Bruvo distance trees but the MLG function would not define them as the same MLG. Is there an option to define MLGs on the basis of Bruvo distance thresholds? For example 0.0 to 0.10? This would be nice function and I welcome your thoughts - if you or others have invented this wheel there is no need for us to do so again. Regards David
Zhian Kamvar
Jun 27, 2014, 1:51:31 PM6/27/14
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Hi David,
Thank you for your suggestion. This indeed is an important feature and we have been considering it for some time now. We are preparing to begin testing this feature in the development version. I will post here as soon as we have a working prototype function available.
Best,
Zhian
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