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</o:shapelayout></xml><![endif]--></head><body lang=EN-GB link=blue vlink=purple><div class=WordSection1><p class=MsoNormal><span style='font-family:"Tahoma","sans-serif"'>Hi,<o:p></o:p></span></p><p class=MsoNormal><span style='font-family:"Tahoma","sans-serif"'><o:p> </o:p></span></p><p class=MsoNormal><span style='font-family:"Tahoma","sans-serif"'>I’m very new to adegenet, and trying to determine if it is sensible to create a distance matrix from a neighbour joining tree (njt) for correspondence analysis with a genetic matrix. I couldn’t find any information on this from a search of the archives. <o:p></o:p></span></p><p class=MsoNormal><span style='font-family:"Tahoma","sans-serif"'><o:p> </o:p></span></p><p class=MsoNormal><span style='font-family:"Tahoma","sans-serif"'>I have created a neighbour joining tree and then used it in an sPCA as follows:<o:p></o:p></span></p><p class=MsoNormal><span style='font-family:"Tahoma","sans-serif"'><o:p> </o:p></span></p><p class=MsoNormal><span style='font-family:"Tahoma","sans-serif"'>njt <- chooseCN(myind@other$xy,ask=FALSE,type=4) #create njt from xy<o:p></o:p></span></p><p class=MsoNormal><span style='font-family:"Tahoma","sans-serif"'>njt_ed<-edit.nb(njt,myind@other$xy,polys=rb_polys) #edit njt to insert “barriers”, creates a “forest”<o:p></o:p></span></p><p class=MsoNormal><span style='font-family:"Tahoma","sans-serif"'>myspca<-spca(myind, cn=njt_ed, scale=TRUE, type=1, plot.nb=TRUE, nfposi=40, nfnega=40, ask=FALSE, scannf=FALSE)<o:p></o:p></span></p><p class=MsoNormal><span style='font-family:"Tahoma","sans-serif"'><o:p> </o:p></span></p><p class=MsoNormal><span style='font-family:"Tahoma","sans-serif"'>I can now create a genetic distance matrix from the microsatellite data:<o:p></o:p></span></p><p class=MsoNormal><span style='font-family:"Tahoma","sans-serif"'>dg<-dist(myind$tab)<o:p></o:p></span></p><p class=MsoNormal><span style='font-family:"Tahoma","sans-serif"'><o:p> </o:p></span></p><p class=MsoNormal><span style='font-family:"Tahoma","sans-serif"'>However, I don’t know how to create a distance matrix for the individuals based on the edited neighbour joining tree, rather than the xy coordinates (as in the tutorial) or the results of the sPCA which also represent genetic variation. I want to compare distances for individuals based on the njt “forest”, so that I can compare them, e.g.:<o:p></o:p></span></p><p class=MsoNormal><span style='font-family:"Tahoma","sans-serif"'><o:p> </o:p></span></p><p class=MsoNormal><span style='font-family:"Tahoma","sans-serif"'>plot(dg,?? geographic distance matrix using njt ??)<o:p></o:p></span></p><p class=MsoNormal><span style='font-family:"Tahoma","sans-serif"'><o:p> </o:p></span></p><p class=MsoNormal><span style='font-family:"Tahoma","sans-serif"'>Perhaps it would be more sensible to use a different type of connection network?<o:p></o:p></span></p><p class=MsoNormal><span style='font-family:"Tahoma","sans-serif"'><o:p> </o:p></span></p><p class=MsoNormal><span style='font-family:"Tahoma","sans-serif"'>If anyone can help I’d be very grateful, thanks.<o:p></o:p></span></p><p class=MsoNormal><span style='font-family:"Tahoma","sans-serif"'><o:p> </o:p></span></p><p class=MsoNormal><span style='font-family:"Tahoma","sans-serif"'>Peter<o:p></o:p></span></p></div></body></html>