API for GuangchuangYu/treeio
Base Classes and Functions for Phylogenetic Tree Input and Output

Global functions
%>% Man page
.BStringSet2bin Source code
.onAttach Source code
BEAST Source code
MRCA Man page
MRCA.phylo Source code
MRCA.treedata Source code
Nnode Man page
Nnode.treedata Man page Source code
Nnode2 Man page
Ntip Man page
Ntip.treedata Source code
ancestor Man page
ancestor.phylo Source code
ancestor.treedata Source code
as.phylo Man page
as.phylo.ggtree Source code
as.phylo.igraph Source code
as.phylo.phylo4 Source code
as.phylo.tbl_df Source code
as.treedata Man page
as.treedata.ggtree Source code
as.treedata.phylo Man page Source code
as.treedata.phylo4 Source code
as.treedata.phylo4d Source code
as.treedata.pml Man page Source code
as.treedata.tbl_df Source code
as_tibble Man page
check_edgelist Source code
child Man page
child.phylo Source code
child.treedata Source code
data_frame Man page
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
drop.tip.treedata Source code
extract.placement Source code
filename Source code
full_join Man page
full_join.phylo Source code
full_join.treedata Source code
get.data Man page
get.fields Man page
get.placements Man page Source code
get.placements.jplace Man page Source code
get.subs_ Source code
get.tree Man page Source code
get.treetext Man page
get.treetext,treedata-method Man page
getNodeName Source code
getNodeNum Man page Source code
getPhyInfo Source code
getSubsLabel Source code
get_seqtype Source code
getnewplacements Source code
getplacedf Source code
gfocus Source code
groupClade.phylo Source code
groupClade.treedata Source code
groupOTU.phylo Source code
groupOTU.treedata Source code
guess_fasta_type Source code
is.ggtree Man page Source code
is.rooted Man page
is.rooted.treedata Source code
isTip Man page Source code
isTip.phylo Man page Source code
isTip.tbl_tree Man page Source code
isTip.treedata Man page
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
mergenm Source code
nodeIds Source code
nodeid Man page
nodeid.phylo Source code
nodeid.treedata Source code
nodelab Man page
nodelab.phylo Source code
nodelab.treedata Source code
offspring Man page
offspring.phylo Source code
offspring.treedata Source code
parent Man page
parent.phylo Source code
parent.treedata Source code
pmlToSeqString Source code
print.beastList Man page Source code
raxml2nwk Man page Source code
read.astral 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.fasta Man page Source code
read.hyphy Man page Source code
read.hyphy.seq Man page Source code
read.iqtree Man page Source code
read.jplace Man page Source code
read.jtree Man page Source code
read.mega Man page
read.mega_tabular Man page Source code
read.mrbayes Man page
read.newick Man page Source code
read.nexus Man page
read.nhx Man page Source code
read.paml_rst Man page Source code
read.phylip Man page Source code
read.phylip.seq Man page Source code
read.phylip.tree Man page Source code
read.phyloT Man page Source code
read.r8s Man page Source code
read.raxml Man page Source code
read.tip_seq_mlc Source code
read.tree Man page
reexports Man page
rename_taxa Man page Source code
reroot_node_mapping Source code
rescale_tree Man page Source code
root Man page
root.phylo Man page Source code
root.treedata Man page Source code
rootnode Man page
rootnode.phylo Source code
rootnode.treedata Source code
rtree Man page
set_branch_length Source code
set_substitution Source code
sibling.phylo Source code
string2DNAbin Source code
summarize_placement Source code
tipIds Source code
tree_subset Man page Source code
tree_subset.phylo Man page Source code
tree_subset.treedata Man page Source code
tree_subset_internal Source code
treedata Man page
write.beast Man page Source code
write.jplace Man page Source code
write.jtree Man page Source code
write.nexus Man page
write.tree Man page
write_beast_newick Source code
GuangchuangYu/treeio documentation built on Nov. 6, 2019, 10:49 a.m.