Re: [R-sig-phylo] recreating sc3.png from screenshot page

[Emmanuel Paradis]

Hi Kevin

If you look carefully at the figure on the web site, you should see that 
both trees have the same topology: they are plotted in different ways. 
You can also see that the screenshot was taken some time ago: the code 
of nj() has been improved since then to avoid this (among other things).

Best,

Emmanuel

Le 18/03/2014 12:13, Kevin Livingstone a écrit :
I'm trying to recreate the screenshot that illustrates the different
trees obtained by the K80 and TN93 models
<http://ape-package.ird.fr/image/sc3.png> for a class exercise, but both
of my output trees are the same. Here's the code I'm entering:

 > library(ape)
 > data(woodmouse)
 > M.K80 <- dist.dna(woodmouse,model="K80")
 > M.TN93 <- dist.dna(woodmouse, model="TN93")
 > tr.K80 <- nj(M.K80)
 > tr.TN93 <- nj(M.TN93)
 > layout(matrix(1:2,1))
 > plot(tr.K80)
 > plot(tr.TN93)

I have attached the output figure, and both trees appear to match the
TN93 tree from the original figure. I'm concerned this means I have
missed or mis-installed something big.

thanks!
-Kevin


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