Table 7.
Tree viewers and phylogenies
| Tool and references | Description | URL |
|---|---|---|
| ARB [123] | A graphically oriented package comprising various tools for sequence database handling and data analysis | http://www.arb-home.de/ |
| Bio.Phylo [286] | A unified toolkit for processing, analyzing and visualizing phylogenetic trees in Biopython | http://biopython.org |
| Dendroscope [125] | Software for visualizing phylogenetic trees and rooted networks | http://ab.inf.uni-tuebingen.de/software/dendroscope/ |
| ETE Toolkit [287] | Python programming toolkit that assists in the automated manipulation, analysis and visualization of phylogenetic and other types of trees | http://etetoolkit.org/ |
| EvolView [288] | Tool for displaying, managing and customizing phylogenetic trees | http://www.evolgenius.info/evolview.html |
| iTOL [126] | Online tool for the display and manipulation of phylogenetic trees | http://itol.embl.de/ |
| MEGA [122] | Integrated tool for phylogenetic analysis and visualization | http://www.megasoftware.net/ |
| NJplot [124] | A tree drawing program able to draw any phylogenetic tree expressed in the Newick phylogenetic tree format | http://doua.prabi.fr/software/njplot |
| OneZoom [289] | Committed to heightening awareness about the diversity of life on earth and its evolutionary history | http://www.onezoom.org/ |
| Paloverde [290] | 3D visualization of phylogenetic structure of moderately large trees on the scale of 100–2500 leaf nodes | http://loco.biosci.arizona.edu/paloverde/paloverde.html |
| PhyloDraw [291] | Drawing tool for creating phylogenetic trees | http://jade.cs.pusan.ac.kr/phylodraw/ |
| PhyloExplorer [292] | Tool to facilitate assessment and management of phylogenetic tree collections | http://www.ncbi.orthomam.univ-montp2.fr/phyloexplorer/ |
| PhyloWidget [293] | Program for viewing, editing and publishing phylogenetic trees online | http://www.phylowidget.org/ |
| TreeDyn [294] | TreeDyn links unique leaf labels to lists of variables/values pairs of annotations, independently of the tree topologies | http://www.treedyn.org/ |
| TreeGraph [295] | A graphical editor for phylogenetic trees that allows many graphical formats for the elements of the tree | http://treegraph.bioinfweb.info/ |
| TreeQ-Vista [296] | Designed for presenting functional annotations in a phylogenetic context | http://genome.lbl.gov/vista/TreeQVista/ |
| TreeVector [297] | Web utility to create and integrate phylogenetic trees as Scalable Vector Graphics (SVG) files | http://supfam.cs.bris.ac.uk/TreeVector/ |
| TreeVolution [298] | Java tool to support visual analysis of phylogenetic trees | http://vis.usal.es/treevolution |
| T-REX [299] | Web server dedicated to the reconstruction of phylogenetic trees and reticulation networks and to the inference of horizontal gene transfer events | http://www.trex.uqam.ca/ |
| ViPhy [300] | Comparison of multiple phylogenetic trees | http://www.gris.tu-darmstadt.de/research/vissearch/projects/ViPhy/ |