%<%                     %<%
%<+%                    %<+%
%>%                     pipe
.                       .
Date2decimal            Date2decimal
NJ                      NJ
add_colorbar            add_colorbar
add_legend              add_legend
aes                     creates a lists of unevaluated expressions
annotation_clade        annotation_clade
annotation_clade2       annotation_clade2
annotation_image        annotation_image
as.binary               as.binary
as.data.frame.phylo     as.data.frame
beast-class             Class "beast" This class stores information of
                        beast output
codeml-class            Class "codeml" This class stores information of
                        output from codeml
codeml_mlc-class        Class "codeml_mlc" This class stores
                        information of mlc file frm codeml output
collapse                collapse
decimal2Date            decimal2Date
download.phylopic       download.phylopic
expand                  expand
flip                    flip
fortify.phylo           fortify
geom_aline              geom_aline
geom_hilight            geom_hilight
geom_nodepoint          geom_nodepoint
geom_rootpoint          geom_rootpoint
geom_text               text annotations
geom_tiplab             geom_tiplab
geom_tippoint           geom_tippoint
geom_tree               geom_tree
get.fields              get.fields method
get.offspring.tip       get.offspring.tip
get.path                get.path
get.phylopic            get.phylopic
get.placements          get.placements method
get.subs                get.subs method
get.tipseq              get.tipseq method
get.tree                get.tree method
get.treeinfo            get.treeinfo method
get.treetext            get.treetext method
getNodeNum              getNodeNum
getRoot                 getRoot
get_taxa_name           get_taxa_name
ggplotGrob              generate a ggplot2 plot grob
ggtree                  visualizing phylogenetic tree and heterogenous
                        associated data based on grammar of graphics
                        'ggtree' provides functions for visualizing
                        phylogenetic tree and its associated data in R.
gheatmap                gheatmap
gplot                   gplot
groupClade              groupClade method
groupOTU                groupOTU method
groupOTU.phylo          groupOTU.phylo
gzoom                   gzoom method
gzoom.phylo             gzoom
hilight                 hilight
hyphy-class             Class "hyphy" This class stores information of
                        HYPHY output
jplace-class            Class "jplace" This class stores information of
                        jplace file.
mask                    mask
merge_tree              merge_tree
msaplot                 msaplot
paml_rst-class          Class "paml_rst" This class stores information
                        of rst file from PAML output
phylopic                phylopic
plot                    plot method
r8s-class               Class "r8s" This class stores output info from
                        r8s
raxml-class             Class "raxml" This class stores RAxML
                        bootstrapping analysis result
read.baseml             read.baseml
read.beast              read.beast
read.codeml             read.codeml
read.codeml_mlc         read.codeml_mlc
read.hyphy              read.hyphy
read.jplace             read.jplace
read.paml_rst           read.paml_rst
read.r8s                read.r8s
read.raxml              read.raxml
read.tree               read newick tree
reroot                  reroot method
rm.singleton.newick     rm.singleton.newick
rotate                  rotate
rtree                   generate random tree
scaleClade              scaleClade
scale_color             scale_color method
scale_x_ggtree          scale_x_ggtree
show,raxml-method       show method
subview                 subview
theme_transparent       theme_transparent
theme_tree              theme_tree
theme_tree2             theme_tree2
write.jplace            write.jplace
