ggtree-package	ggtree
%<%	update.TREE
%<+%	add.TREEDATA
%>%	pipe
.	dotFun
add_colorbar	add_colorbar
add_legend	add_legend
aes	aes
annotation_clade	annotation_clade
annotation_clade2	annotation_clade2
annotation_image	annotation_image
as.binary	as.binary
as.binary.phylo	as.binary
as.data.frame.phylo	as.data.frame.phylo
beast-class	beast-class
codeml-class	codeml-class
codeml_mlc-class	codeml_mlc-class
collapse	collapse
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	geom_text
geom_tiplab	geom_tiplab
geom_tippoint	geom_tippoint
geom_tree	geom_tree
get.fields	get.fields-methods
get.fields,beast-method	get.fields-methods
get.fields,codeml-method	get.fields-methods
get.fields,codeml_mlc-method	get.fields-methods
get.fields,hyphy-method	get.fields-methods
get.fields,jplace,ANY-method	get.fields-methods
get.fields,jplace-method	jplace-class
get.fields,paml_rst-method	get.fields-methods
get.offspring.tip	get.offspring.tip
get.path	get.path
get.phylopic	get.phylopic
get.placements	get.placements-methods
get.placements,jplace,ANY-method	get.placements-methods
get.placements,jplace-method	jplace-class
get.subs	get.subs-methods
get.subs,codeml-method	get.subs-methods
get.subs,hyphy-method	get.subs-methods
get.subs,paml_rst-method	get.subs-methods
get.tipseq	get.tipseq-methods
get.tipseq,codeml-method	get.tipseq-methods
get.tipseq,paml_rst-method	get.tipseq-methods
get.tree	get.tree-methods
get.tree,beast	get.tree-methods
get.tree,beast-method	beast-class
get.tree,codeml-method	get.tree-methods
get.tree,codeml_mlc-method	get.tree-methods
get.tree,hyphy-method	get.tree-methods
get.tree,jplace-method	get.tree-methods
get.tree,paml_rst-method	get.tree-methods
get.tree,phylo-method	get.tree-methods
get.treeinfo	get.treeinfo-methods
get.treeinfo,jplace,ANY-method	get.treeinfo-methods
get.treeinfo,jplace-method	jplace-class
get.treetext	get.treetext-methods
get.treetext,jplace,ANY-method	get.treetext-methods
get.treetext,jplace-method	jplace-class
getNodeNum	getNodeNum
getRoot	getRoot
get_taxa_name	get_taxa_name
ggplotGrob	ggplotGrob
ggtree	ggtree
gheatmap	gheatmap
gplot	gplot
groupClade	groupClade-methods
groupClade,beast-method	groupClade-methods
groupClade,codeml-method	groupClade-methods
groupClade,codeml_mlc-method	groupClade-methods
groupClade,gg-method	groupClade-methods
groupClade,ggplot-method	groupClade-methods
groupClade,hyphy-method	groupClade-methods
groupClade,jplace-method	groupClade-methods
groupClade,paml_rst-method	groupClade-methods
groupClade,phylo-method	groupClade-methods
groupOTU	groupOTU-methods
groupOTU,beast-method	groupOTU-methods
groupOTU,codeml-method	groupOTU-methods
groupOTU,codeml_mlc-method	groupOTU-methods
groupOTU,gg-method	groupOTU-methods
groupOTU,ggplot-method	groupOTU-methods
groupOTU,hyphy-method	groupOTU-methods
groupOTU,jplace-method	groupOTU-methods
groupOTU,paml_rst-method	groupOTU-methods
groupOTU,phylo-method	groupOTU-methods
groupOTU.phylo	groupOTU.phylo
gzoom	gzoom-methods
gzoom,beast-method	gzoom-methods
gzoom,codeml-method	gzoom-methods
gzoom,codeml_mlc-method	gzoom-methods
gzoom,hyphy-method	gzoom-methods
gzoom,paml_rst-method	gzoom-methods
gzoom,phylo-method	gzoom-methods
gzoom.phylo	gzoom.phylo
hilight	hilight
hyphy-class	hyphy-class
jplace-class	jplace-class
mask	mask
merge_tree	merge_tree
msaplot	msaplot
NJ	NJ
package-ggtree	ggtree
paml_rst-class	paml_rst-class
phylopic	phylopic
plot	plot-methods
plot,beast,ANY-method	plot-methods
plot,codeml,ANY-method	plot-methods
plot,codeml_mlc,ANY-method	plot-methods
plot,hyphy,ANY-method	plot-methods
plot,paml_rst,ANY-method	plot-methods
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.tree	read.tree
reroot	reroot-methods
reroot,beast-method	reroot-methods
reroot,phylo-method	reroot-methods
rm.singleton.newick	rm.singleton.newick
rotate	rotate
rtree	rtree
scaleClade	scaleClade
scale_color	scale_color-methods
scale_color,beast-method	scale_color-methods
scale_color,codeml-method	scale_color-methods
scale_color,codeml_mlc-method	scale_color-methods
scale_color,hyphy-method	scale_color-methods
scale_color,jplace-method	scale_color-methods
scale_color,paml_rst-method	scale_color-methods
scale_color,phylo-method	scale_color-methods
scale_x_ggtree	scale_x_ggtree
set.subs,paml_rst-method	paml_rst-class
set.subs<-,paml_rst-method	paml_rst-class
show	show-methods
show,beast-method	show-methods
show,codeml-method	show-methods
show,codeml_mlc-method	show-methods
show,hyphy-method	show-methods
show,jplace-method	jplace-class
show,paml_rst-method	show-methods
subview	subview
theme_transparent	theme_transparent
theme_tree	theme_tree
theme_tree2	theme_tree2
write.jplace	write.jplace
