Tree visualization software tools | Phylogenomics data analysis
Phylogenetic trees are complex data forms that need to be graphically displayed to be human-readable. Traditional techniques of plotting phylogenetic trees focus on rendering a single static image, but increases in the production of biological data and large-scale analyses demand scalable, browsable, and interactive trees.
Displays phylogenetic trees and constructs publication-ready figures. FigTree is implemented to visualize summarized and annotated trees produced by BEAST. It offers options to view shapes for internal or external nodes or both.
A tool using annotations and dynamic graphical methods for editing and analyzing multiple trees. The main features of TreeDyn are 1) the management of multiple windows and multiple trees per window, 2) the export of graphics to several standard file formats with or without HTML encapsulation and a new format called TGF, which enables saving and restoring graphical analysis, 3) the projection of texts or symbols facing leaf labels or linked to nodes, through manual pasting or by using annotation files, 4) the highlight of graphical elements after querying leaf labels (or annotations) or by selection of graphical elements and information extraction, 5) the highlight of targeted trees according to a source tree browsed by the user, 6) powerful scripts for automating repetitive graphical tasks, 7) a command line interpreter enabling the use of TreeDyn through CGI scripts for online building of trees, 8) the inclusion of a library of packages dedicated to specific research fields involving trees.
A user-friendly software that allows the combined analysis of multiple data sources for microbial epidemiological and population studies. PHYLOViZ Online was developed to allow users to do these analyses without software installation and to enable easy accessing and sharing of data and analyses results from any Internet enabled computer. PHYLOViZ Online also offers a RESTful API for programmatic access to data and algorithms, allowing it to be seamlessly integrated into any third party web service or software.
Provides several tools for sequence database maintenance and analysis. ARB is a graphically oriented package that consists of software tools directly interacting with one another as well as the central database, which are controlled via a common graphical interface. It includes software for visualization, sequence edition, profiles determination, filtering, phylogenetic treeing, sequence alignment, probe design and evaluation and data import and export.
Allows users to draw and compare rooted phylogenetic networks. Dendroscope is a program that includes characteristics allowing researchers to treat realistic phylogenetic trees. It also provides an interactive platform for researchers to explore the application of rooted phylogenetic networks to their phylogenetic trees and data. Moreover, this tool is available with a graphical user interface (GUI) or a command line interface (CLI).
A package for diversity and phylogenetic analysis on the basis of evolutionary dissimilarities. DARwin is mainly focused on diversity structure description based on distance methods, organized in five parts: dissimilarity measure, tree construction from dissimilarities, tree representation and edition, tree comparison, and sampling procedures to minimize disequilibria in a collection.