Paloverde: An OpenGL 3D phylogeny browser

Michael J. Sanderson

doi:10.1093/bioinformatics/btl044

Paloverde: An OpenGL 3D phylogeny browser

Michael J. Sanderson

Research output: Contribution to journal › Article › peer-review

20 Scopus citations

Abstract

Summary: 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.

Original language	English (US)
Pages (from-to)	1004-1006
Number of pages	3
Journal	Bioinformatics
Volume	22
Issue number	8
DOIs	https://doi.org/10.1093/bioinformatics/btl044
State	Published - Apr 2006
Externally published	Yes

ASJC Scopus subject areas

Statistics and Probability
Biochemistry
Molecular Biology
Computer Science Applications
Computational Theory and Mathematics
Computational Mathematics

Access to Document

10.1093/bioinformatics/btl044

Cite this

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title = "Paloverde: An OpenGL 3D phylogeny browser",

abstract = "Summary: 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.",

author = "Sanderson, \{Michael J.\}",

note = "Funding Information: Paloverde is part of the Phylota project (http://www.phylota.org), supported by the NSF AToL program. Thanks to Gordon Burleigh, Oliver Eulenstein, David Fernandez-Baca, Amy Driskell, Taum Hanlon, Junhyong Kim, Shelley McMahon, Brian O{\textquoteright}Meara, Cam Webb and Marty Wojciechowski for feedback on the program design.",

year = "2006",

month = apr,

doi = "10.1093/bioinformatics/btl044",

language = "English (US)",

volume = "22",

pages = "1004--1006",

journal = "Bioinformatics",

issn = "1367-4803",

publisher = "Oxford University Press",

number = "8",

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T2 - An OpenGL 3D phylogeny browser

AU - Sanderson, Michael J.

N1 - Funding Information: Paloverde is part of the Phylota project (http://www.phylota.org), supported by the NSF AToL program. Thanks to Gordon Burleigh, Oliver Eulenstein, David Fernandez-Baca, Amy Driskell, Taum Hanlon, Junhyong Kim, Shelley McMahon, Brian O’Meara, Cam Webb and Marty Wojciechowski for feedback on the program design.

PY - 2006/4

Y1 - 2006/4

N2 - Summary: 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.

AB - Summary: 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.

UR - https://www.scopus.com/pages/publications/33645801601

UR - https://www.scopus.com/pages/publications/33645801601#tab=citedBy

U2 - 10.1093/bioinformatics/btl044

DO - 10.1093/bioinformatics/btl044

M3 - Article

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AN - SCOPUS:33645801601

SN - 1367-4803

VL - 22

SP - 1004

EP - 1006

JO - Bioinformatics

JF - Bioinformatics

IS - 8

ER -

Paloverde: An OpenGL 3D phylogeny browser

Abstract

ASJC Scopus subject areas

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