To fill this gap, we developed ggtree ( Yu et al., 2017), a package for the R programming language ( R Core Team, 2016) released under the Bioconductor project ( Gentleman et al., 2004). ![]() Therefore, in addition to standalone applications that focus on each of the specific analysis and data types, researchers studying molecular evolution need a robust and programmable platform that allows the high levels of integration and visualization of many of these different aspects of data (raw or from other primary analyses) over the phylogenetic trees to identify their associations and patterns. For instance, the influenza virus has a wide host range, diverse and dynamic genotypes, and characteristic transmission behaviors that are mostly associated with the virus’s evolution and essentially among themselves. ![]() ![]() As phylogenetic trees are becoming more widely used in multidisciplinary studies, there is an increasing need to incorporate various types of phylogenetic covariates and other associated data from different sources into the trees for visualizations and further analyses. However, their pre-defined annotating functions are usually limited to some specific phylogenetic data. ![]() Only a few of them, such as FigTree, TreeDyn and iTOL, allow users to annotate the trees with colored branches, highlighted clades with tree features. There are many software packages and web tools that are designed for displaying phylogenetic trees, such as TreeView ( Page, 2002), FigTree, TreeDyn ( Chevenet et al., 2006), Dendroscope ( Huson & Scornavacca, 2012), EvolView ( He et al., 2016), and iTOL ( Letunic & Bork, 2007), etc.
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