Here’s a handy little Perl script I wrote that takes a nexus formatted tree file and breaks down every tree that it finds into the clades that it is composed of (i.e., every node in the starting tree is returned as a new tree). It spits all of these out into a text file, which can then be copied and pasted into a tree block.

Each tree in the original file gets its own text file, named woodchipper_treename.tre, where “treename” is the name of the tree given in the trees block in the input file.

It hasn’t been tested exhaustively yet, so please check the results and contact me if you run into any trouble. No warranty is expressed or implied, your mileage may vary, not valid where prohibited, and all that.

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