Paloverde: an OpenGL 3D phylogeny browser | Zendy

Michael J. Sanderson | Zendy

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Paloverde: an OpenGL 3D phylogeny browser

Author(s) -

Michael J. Sanderson

Publication year - 2006

Publication title -

bioinformatics

Language(s) - English

Resource type - Journals

SCImago Journal Rank - 3.599

H-Index - 390

eISSN - 1367-4811

pISSN - 1367-4803

DOI - 10.1093/bioinformatics/btl044

Subject(s) - opengl , computer science , os x , computer graphics (images) , zoom , tree (set theory) , visualization , graphical user interface , node (physics) , mac os , phylogenetic tree , programming language , software , operating system , biology , combinatorics , data mining , mathematics , physics , lens (geology) , paleontology , biochemistry , quantum mechanics , gene

Paloverde is a new program designed to help visualize the phylogenetic structure of moderately large trees--trees on the scale of 100-2500 leaf nodes. The program embeds the user in an interactive virtual 3D world in which a large tree presented in various layouts can be manipulated through a mouse interface. The program implements radial 2D layouts, and true 3D spiral, conical and hemispherical (i.e. truly 'tree'-like) layouts. Subclades can be defined in the input file (using standard node-based definitions) and displayed collapsed as new leaf nodes, or left intact but annotated with names around the periphery of the tree. A search tool lets the user zoom to any selected leaf node. Paloverde is an open source project written in ANSI C using the OpenGL library for 3D visualization.

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