TreeJuxtaposer 

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TreeJuxtaposer lets you interactively view a single tree, or compare two or more trees.

It handles all kinds of trees, including phylogenetic trees, taxonomic trees, consensus trees, dendrograms from cluster hierarchies, and others.

Uses nested parentheses (Newick/New Hampshire) data format.

Guaranteed visibility of marked regions provides visual landmarks.

Structural differences are automatically marked, and the marked clades highlight corresponding nodes on the trees through the use of a generalization of the Robinson-Foulds distance metric.

Responsive drawing for even very large trees with advanced graphics techniques.

Multi-platform: runs on Linux, Mac and Windows.