Archaeopteryx is an interactive computer software program, written in Java, for viewing, editing, and analyzing phylogenetic trees. This type of program can be used for a variety of analyses of molecular data sets, but is particularly designed for phylogenomics. Besides tree description formats with limited expressiveness (such as Newick/New Hamphshire, Nexus), ATV also implements the phyloXML format. Archaeopteryx is the successor to the tree viewer ATV.
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“Is not disease the rule of existence? There is not a lily pad floating on the river but has been riddled by insects. Almost every shrub and tree has its gall, oftentimes esteemed its chief ornament and hardly to be distinguished from the fruit. If misery loves company, misery has company enough. Now, at midsummer, find me a perfect leaf or fruit.”
—Henry David Thoreau (1817–1862)