However these packages were designed for epidemiology and microbiome data respectively and did not aim to provide a general solution for tree visualization and annotation. The ggplot2 system of graphics allows rapid customization and exploration of design solutions. 2014) and phyloseq (McMurdie and Holmes 2013) extended ggplot2 to plot phylogenetic trees. However, the base graphics system is relatively difficult to extend and limits the complexity of tree figure to be displayed. In particular, ape is one of the fundamental package for phylogenetic analysis and data processing. Some packages, including ape (Paradis, Claude, and Strimmer 2004) and phytools (Revell 2012), which are capable of displaying and annotating trees, are developed using the base graphics system of R. Most of the R packages in phylogenetics focus on specific statistical analyses rather than viewing and annotating the trees with more generalized phylogeny-associated data. However, a comprehensive package, designed for viewing and annotating phylogenetic trees, particularly with complex data integration, is not yet available. The R language is increasingly being used in phylogenetics. The ggtree is built to work with phylogenetic data object generated by treeio, and display tree graphics with ggplot2 package (Wickham 2016) that was based on the grammar of graphics (Wilkinson et al. To fill this gap, we developed ggtree, a package for the R programming language (R Core Team 2016) released under the Bioconductor project (Gentleman et al. Therefore, in addition to standalone applications that focus on each of the specific analysis and data type, researchers studying molecular evolution need a robust and programmable platform that allows the high levels 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, influenza virus has a wide host range, diverse and dynamic genotypes and characteristic transmission behaviors that are mostly associated with the virus evolution and essentially among themselves. As phylogenetic trees become more widely used in multidisciplinary studies, there is an increasing need to incorporate various types of the 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 several of them, such as FigTree, TreeDyn and iTOL, allow users to annotate the trees with coloring branches, highlighted clades and tree features. 2016) and iTOL (Letunic and Bork 2007), etc. 2006), Dendroscope (Huson and Scornavacca 2012), EvolView (Z.
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There are many software packages and webtools that are designed for displaying phylogenetic trees, such as TreeView (2), FigTree 7, TreeDyn (Chevenet et al.