primetv: a viewer for reconciled trees

We have developed a new reconciliation viewer, primetv. It is a simple and compact visualization program that is the first automatic tool for illustrating general tree reconciliations. It reads reconciled trees in an extended Newick format and outputs them as tree-within-tree illustrations in a range of graphic formats. Output attributes, such as colors and layout, can easily be adjusted by the user. To enhance the construction of input to primetv, two helper programs, readReconciliation and reconcile, accompany primetv. Detailed examples of all programs' usage are provided in the text. For the casual user a web-service provides a simple user interface to all programs.With primetv, the first visualization tool for general reconciliations, illustrations of trees-within-trees are easy to produce. Because it clarifies and accentuates an underlying structure in a reconciled tree, e.g., the impact of a species tree on a gene-family phylogeny, it will enhance scientific presentations as well as pedagogic illustrations in an educational setting. primetv is available at http://prime.sbc.su.se/primetv webcite, both as a standalone command-line tool and as a web service. The software is distributed under the GNU General Public License.Illustrating evolution using phylogenetic trees is a natural way of depicting evolutionary processes. Indeed, already Darwin drew trees and there exist many tools for automatically producing graphical representations of phylogenies. Some phenomena are, however, better viewed as trees-within-trees. For example, gene family evolution should be put in the context of species evolution, parasite evolution is best understood in relation to a host tree, and a speciation process that is affected by geological processes, such as continental breakup and movement, is often viewed as a species tree that evolves within an area tree. The relation between the two trees is called a reconciliation [1]. More precise, a reconciliation describes how a guest tree, G