ggtree-package	ggtree
%<%	update-TREE
%<+%	add-TREEDATA
%>%	pipe
.	dotFun
add_colorbar	add_colorbar
annotation_image	annotation_image
apeBoot	apeBoot
apeBootstrap-class	apeBootstrap-class
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
Date2decimal	Date2decimal
decimal2Date	decimal2Date
download.phylopic	download.phylopic
expand	expand
flip	flip
fortify.phylo	fortify
geom_aline	geom_aline
geom_cladelabel	geom_cladelabel
geom_hilight	geom_hilight
geom_nodepoint	geom_nodepoint
geom_point2	geom_point2
geom_rootpoint	geom_rootpoint
geom_segment2	geom_segment2
geom_text2	geom_text2
geom_tiplab	geom_tiplab
geom_tippoint	geom_tippoint
geom_tree	geom_tree
geom_tree2	geom_tree2
geom_treescale	geom_treescale
get.fields	get.fields-methods
get.fields,apeBootstrap-method	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,nhx-method	get.fields-methods
get.fields,paml_rst-method	get.fields-methods
get.fields,phangorn-method	get.fields-methods
get.fields,r8s-method	get.fields-methods
get.fields,raxml-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.subs,phangorn-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,apeBootstrap-method	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,nhx-method	get.tree-methods
get.tree,paml_rst-method	get.tree-methods
get.tree,phangorn-method	get.tree-methods
get.tree,phylip-method	get.tree-methods
get.tree,phylo-method	get.tree-methods
get.tree,r8s-method	get.tree-methods
get.tree,raxml-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_clade_position	get_clade_position
get_heatmap_column_position	get_heatmap_column_position
get_taxa_name	get_taxa_name
ggtree	ggtree
gheatmap	gheatmap
groupClade	groupClade-methods
groupClade,apeBootstrap-method	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,nhx-method	groupClade-methods
groupClade,paml_rst-method	groupClade-methods
groupClade,phangorn-method	groupClade-methods
groupClade,phylip-method	groupClade-methods
groupClade,phylo-method	groupClade-methods
groupClade,r8s-method	groupClade-methods
groupClade,raxml-method	groupClade-methods
groupOTU	groupOTU-methods
groupOTU,apeBootstrap-method	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,nhx-method	groupOTU-methods
groupOTU,paml_rst-method	groupOTU-methods
groupOTU,phangorn-method	groupOTU-methods
groupOTU,phylip-method	groupOTU-methods
groupOTU,phylo-method	groupOTU-methods
groupOTU,r8s-method	groupOTU-methods
groupOTU,raxml-method	groupOTU-methods
groupOTU.phylo	groupOTU.phylo
gzoom	gzoom-methods
gzoom,apeBootstrap-method	gzoom-methods
gzoom,beast-method	gzoom-methods
gzoom,codeml-method	gzoom-methods
gzoom,codeml_mlc-method	gzoom-methods
gzoom,gg-method	gzoom-methods
gzoom,hyphy-method	gzoom-methods
gzoom,nhx-method	gzoom-methods
gzoom,paml_rst-method	gzoom-methods
gzoom,phangorn-method	gzoom-methods
gzoom,phylo-method	gzoom-methods
gzoom,r8s-method	gzoom-methods
gzoom,raxml-method	gzoom-methods
gzoom.phylo	gzoom.phylo
hyphy-class	hyphy-class
inset	inset
jplace-class	jplace-class
mask	mask
merge_tree	merge_tree
MRCA	MRCA
msaplot	msaplot
multiplot	multiplot
nhx-class	nhx-class
NJ	NJ
nodebar	nodebar
nodepie	nodepie
package-ggtree	ggtree
paml_rst-class	paml_rst-class
phangorn-class	phangorn-class
phylip-class	phylip-class
phylopic	phylopic
phyPML	phyPML
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
plot,r8s,ANY-method	plot-methods
plot,raxml,ANY-method	plot-methods
pmlToSeq	pmlToSeq
r8s-class	r8s-class
raxml-class	raxml-class
raxml2nwk	raxml2nwk
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.nhx	read.nhx
read.paml_rst	read.paml_rst
read.phylip	read.phylip
read.r8s	read.r8s
read.raxml	read.raxml
read.tree	read.tree
reroot	reroot-methods
reroot,beast-method	reroot-methods
reroot,phylo-method	reroot-methods
rescale_tree	rescale_tree
rm.singleton.newick	rm.singleton.newick
rotate	rotate
rtree	rtree
scaleClade	scaleClade
scale_color	scale_color-methods
scale_color,apeBootstrap-method	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,nhx-method	scale_color-methods
scale_color,paml_rst-method	scale_color-methods
scale_color,phangorn-method	scale_color-methods
scale_color,phylo-method	scale_color-methods
scale_color,r8s-method	scale_color-methods
scale_color,raxml-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,apeBootstrap-method	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,nhx-method	show-methods
show,paml_rst-method	show-methods
show,phangorn-method	show-methods
show,phylip-method	show-methods
show,r8s-method	show-methods
show,raxml-method	show-methods
StatHilight	ggtree-ggproto
stat_hilight	stat_hilight
subview	subview
theme_inset	theme_inset
theme_transparent	theme_transparent
theme_tree	theme_tree
theme_tree2	theme_tree2
viewClade	viewClade
write.jplace	write.jplace
