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Re: supertree construction in perl

by pvaldes (Chaplain)
on Oct 09, 2012 at 09:00 UTC ( #997955=note: print w/replies, xml ) Need Help??

in reply to supertree construction in perl

If you want to play with the nodes, calculate bootstrap values etc, start with bioperl

But if you want only to plot a nice tree with few nodes and non interactive, you have at least two superb options outside perl. Each time I see the plot that you want to make, something in my mind is whispering at me: this is clearly either a graphviz job...

use graphviz; my $plot = GraphViz->new( layout => 'dot', directed => 0, rankdir => 'TB' ); # dot = directed plot as output, # better than 'neato' for drawing trees

... or either a work for the ever elegant latex

use LaTeX::Driver;

(\usepackage{tikz}). Both can produce the plot that you want, after perl massage and pass the data in an accurate way. Of these, Latex is probably the only that can plot _exactly_ what you show in the picture, but don't underestimate graphviz, it is a solid and very powerful program

And if you have a big structure with many thousands or millions of nodes to plot, R is your man. Graphviz is not designed for this kind of situation.

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