TreeGraph 2: Combining and visualizing evidence from different phylogenetic analyses

By Ben C. Stöver, Kai F. Müller. BMC Bioinformatics, 2010

1,534 citations recorded by the source corpus.

BackgroundToday it is common to apply multiple potentially conflicting data sources to a given phylogenetic problem. At the same time, several different inference techniques are routinely employed instead of relying on just one. In view of both trends it is becoming increasingly important to be able to efficiently compare different sets of statistical values supporting (or conflicting with) the nodes of a given tree topology, and merging this into a meaningful representation. A tree editor supporting this should also allow for flexible editing operations and be able to produce ready-to-publish figures.ResultsWe developed TreeGraph 2, a GUI-based graphical editor for phylogenetic trees (available from http://treegraph.bioinfweb.info). It allows automatically combining information from different phylogenetic analyses of a given dataset (or from different subsets of the dataset), and helps to identify and graphically present incongruences. The program features versatile editing and formatting options, such as automatically setting line widths or colors according to the value of any of the unlimited number of variables that can be assigned to each node or branch. These node/branch data can be imported from spread sheets or other trees, be calculated from each other by specified mathematical expressions, filtered, copied from and to other internal variables, be kept invisible or set visible and then be freely formatted (individually or across the whole tree). Beyond typical editing operations such as tree rerooting and ladderizing or moving and collapsing of nodes, whole clades can be copied from other files and be inserted (along with all node/branch data and legends), but can also be manually added and, thus, whole trees can quickly be manually constructed de novo. TreeGraph 2 outputs various graphic formats such as SVG, PDF, or PNG, useful for tree figures in both publications and presentations.ConclusionTreeGraph 2 is a user-friendly, fully documented application to produce ready-to-publish trees. It can display any number of annotations in several ways, and permits easily importing and combining them. Additionally, a great number of editing- and formatting-operations is available.

Subfields: Ecology, Evolution, Behavior and Systematics, Molecular Biology, Paleontology

View Paper: https://www.semanticscholar.org/paper/adcae8415f73e3992c0313e66c8f466231314f55

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Citations in the corpus

ADAGE-Based Integration of Publicly Available Pseudomonas aeruginosa Gene Expression Data with Denoising Autoencoders Illuminates Microbe-Host Interactions (2016, methodology): “3D were drawn using tree graph 2 (67).”
antiSMASH: rapid identification, annotation and analysis of secondary metabolite biosynthesis gene clusters in bacterial and fungal genome sequences (2011, methodology): “…on the highest-scoring pHMM on its sequence above a certain e -value threshold—the predicted protein sequence is aligned to the smCOG seed alignment, and a rough neighbor-joining phylogenetic tree is calculated using FastTree 2 (23) and visualized with TreeGraph 2 (24) (Supplementary Figure S1).”
Evolview v2: an online visualization and management tool for customized and annotated phylogenetic trees (2016, methodology): “A wide variety of tree visualization software and online tools have thus been developed, such as the ETE toolkit (5), TreeView (6), TreeVector (7), Dendroscope (8), iTol (9), jsPhyloSVG (10), PhyloWidget (11), T-REX (12), Treelink (13), TreeGraph 2 (14) and many others (see https://en.”