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Interpreting large clusters

Hi Phil,

I'd start by asking if you can categorize your species in some sort of  
meaningful manner.  If so you can color code the labels of your  
dendrogram.  The package 'ape' includes 'tip.color=...' as a parameter  
in plot.phylo().  Create a vector of colors or numbers and use that to  
parameterize tip.color.

In regards to viewing the graphic I'd create a pdf.  This allows you  
to parameterize the paper size with width=7 and height=7 (units are  
inches).  You can parameterize this to height=14 or height=28 or other  
large values.  This may be printed over several pages or you can just  
scroll over it on your monitor.

Good luck!