API for Bioconductor-mirror/treeio
Base Classes and Functions for Phylogenetic Tree Input and Output

Global functions
BEAST Source code
Nnode Man page Source code
Nnode2 Man page
Ntip Man page Source code
\%>\% Man page
add_new_line Source code
add_pseudo_nodelabel Source code
append_extraInfo Source code
as.phylo Man page
as.phylo.data.frame Source code
as.phylo.ggtree Source code
as.phylo.phylo4 Source code
as.phylo.treedata Source code
as.treedata Man page Source code
as.treedata.ggtree Source code
as.treedata.phylo Man page Source code
as.treedata.phylo4 Source code
as.treedata.phylo4d Source code
beast-class Man page
codeml-class Man page
codeml_mlc-class Man page
codon2AA Source code
drop.tip Man page
drop.tip,phylo Man page
drop.tip,phylo-method Man page
drop.tip,treedata Man page
drop.tip,treedata-method Man page
edgeNum2nodeNum Source code
fields_wrap Source code
filename Source code
get.fields Man page
get.fields,beast-method Man page
get.fields,codeml-method Man page
get.fields,codeml_mlc-method Man page
get.fields,hyphy-method Man page
get.fields,jplace,ANY-method Man page
get.fields,jplace-method Man page
get.fields,paml_rst-method Man page
get.fields,phangorn-method Man page
get.fields,r8s-method Man page
get.fields,treedata-method Man page
get.fields.jplace Source code
get.fields.tree Source code
get.offspring Source code
get.placements Man page
get.placements,jplace,ANY-method Man page
get.placements,jplace-method Man page
get.subs Man page
get.subs,codeml-method Man page
get.subs,hyphy-method Man page
get.subs,paml_rst-method Man page
get.subs,phangorn-method Man page
get.subs_ Source code
get.subs_paml_rst Source code
get.tipseq Man page
get.tipseq,codeml-method Man page
get.tipseq,paml_rst-method Man page
get.tree Man page
get.tree,beast Man page
get.tree,beast-method Man page
get.tree,codeml-method Man page
get.tree,codeml_mlc-method Man page
get.tree,hyphy-method Man page
get.tree,jplace-method Man page
get.tree,paml_rst-method Man page
get.tree,phangorn-method Man page
get.tree,phylip-method Man page
get.tree,phylo-method Man page
get.tree,r8s-method Man page
get.tree,treedata-method Man page
get.treeinfo,jplace-method Man page
get.treetext Man page
get.treetext,jplace,ANY-method Man page
get.treetext,jplace-method Man page
get.treetext.jplace Source code
getAncestor Source code
getChild Source code
getNodeName Source code
getNodeNum Man page Source code
getParent Source code
getPhyInfo Source code
getRoot Man page Source code
getSibling Source code
getSubsLabel Source code
get_nhx_feature Source code
get_nhx_feature_internal Source code
get_seqtype Source code
get_tree_edge_index_paml Source code
get_tree_edge_paml Source code
get_tree_index_paml Source code
gfocus Source code
groupClade Man page
groupClade,beast-method Man page
groupClade,codeml-method Man page
groupClade,jplace-method Man page
groupClade,phangorn-method Man page
groupClade,phylip-method Man page
groupClade,phylo-method Man page
groupClade,treedata-method Man page
groupClade.phylo Source code
groupClade_ Source code
groupOTU Man page
groupOTU,beast-method Man page
groupOTU,codeml-method Man page
groupOTU,codeml_mlc-method Man page
groupOTU,jplace-method Man page
groupOTU,paml_rst-method Man page
groupOTU,phangorn-method Man page
groupOTU,phylip-method Man page
groupOTU,phylo-method Man page
groupOTU,r8s-method Man page
groupOTU,treedata-method Man page
groupOTU.phylo Man page Source code
groupOTU_ Source code
has.extraInfo Source code
has.field Source code
has.slot Source code
hyphy-class Man page
is.character_beast Source code
is.ggtree Man page Source code
is.tree Source code
is.tree_attribute Source code
is.tree_attribute_ Source code
is_numeric Source code
jplace-class Man page
jplace_treetext_to_phylo Source code
label_branch_paml Man page Source code
mask Man page Source code
matrix2vector.phyDat Source code
matrix2vector.phyDat.item Source code
merge_tree Man page Source code
nodeIds Source code
paml_rst-class Man page
phangorn-class Man page
phyPML Man page Source code
phylip-class Man page
pmlToSeq Man page Source code
pmlToSeqString Source code
print.beastList Man page Source code
print_fields Source code
r8s-class Man page
raxml2nwk Man page Source code
read.ancseq_paml_rst Source code
read.baseml Man page Source code
read.beast Man page Source code
read.codeml Man page Source code
read.codeml_mlc Man page Source code
read.dnds_mlc Source code
read.hyphy Man page Source code
read.jplace Man page Source code
read.newick Man page Source code
read.nhx Man page Source code
read.paml_rst Man page Source code
read.phylip Man page Source code
read.phyloT Man page Source code
read.phylo_paml_mlc Source code
read.phylo_paml_rst Source code
read.r8s Man page Source code
read.raxml Man page Source code
read.stats_beast Source code
read.stats_beast_internal Source code
read.tip_seq_mlc Source code
read.trans_beast Source code
read.tree Man page
read.treetext_beast Source code
read.treetext_paml Source code
read.treetext_paml_mlc Source code
read.treetext_paml_rst Source code
reexports Man page
remove_quote_in_tree_label Source code
rtree Man page
seq2codon Source code
set.hyphy_ Source code
set.paml_rst_ Source code
set.subs,paml_rst-method Man page
set.subs<-,paml_rst-method Man page
show Man page
show,beast-method Man page
show,codeml-method Man page
show,codeml_mlc-method Man page
show,hyphy-method Man page
show,jplace-method Man page
show,paml_rst-method Man page
show,phylip-method Man page
show,r8s-method Man page
show,treedata-method Man page
subs_paml_rst Source code
taxa_rename Man page Source code
tipIds Source code
treedata-class Man page
write.jplace Man page Source code
write.tree Man page
Bioconductor-mirror/treeio documentation built on July 21, 2017, 11:51 a.m.