TreeTools v0.1.3


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Create, Modify and Analyse Phylogenetic Trees

Efficient implementations of functions for the creation, modification and analysis of phylogenetic trees. Applications include: generation of trees with specified shapes; rooting of trees and extraction of subtrees; calculation and depiction of node support; calculation of ancestor-descendant relationships; import and export of trees from Newick, Nexus (Maddison et al. 1997) <doi:10.1093/sysbio/46.4.590>, and TNT <> formats; and analysis of partitions and partition information.

Functions in TreeTools

Name Description Raw data from Zhang et al. 2016
AllAncestors List all ancestral nodes
Cladewise Reorder trees
Lobo.phy Data from Zhang et al. 2016 in phyDat format
CharacterInformation Character information content
AncestorEdge Ancestral edge
ConsensusWithout Consensus without taxa
BalancedTree Generate a Balanced Tree
.DecodeRaw Decode Splits objects
NewickTree Newick Tree
DescendantEdges Descendant Edges
Neworder Reorder edges of a phylogenetic tree
CompatibleSplits Which splits are compatible?
DoubleFactorial Double Factorial
N1Spr Number of trees one SPR step away
EdgeAncestry Edge ancestry
NSplits Number of distinct partitions
NTip Number of tips in a phylogenetic tree
EdgeDistances Distance between edges
SplitMatchProbability Probability of matching this well
NonDuplicateRoot Non-duplicate root
PectinateTree Generate a Pectinate Tree
ReadCharacters Read characters from Nexus file
ReadTntTree Parse TNT Tree
NJTree Neighbour Joining Tree
ApeTime Ape Time
StringToPhyDat String to phyDat
RightmostCharacter Rightmost character of string
RenumberTree Renumber a tree in preorder
Subsplit Subset of a split on fewer taxa
UnrootedTreesMatchingSplit Number of trees consistent with split
TrivialSplits Are splits trivial?
MRCA Most Recent Common Ancestor
ExtractTaxa Extract taxa from a matrix block
SplitFrequency Frequency of splits
EnforceOutgroup Force taxa to form an outgroup
MatrixToPhyDat Matrix to phyDat
RenumberTips Renumber a tree's tips
SortTree Sort tree
NPartitionPairs Distributions of tips consistent with a partition pair
TipsInSplits Tips contained within splits
Renumber Renumber a tree's nodes and tips
SingleTaxonTree SingleTaxonTree
as.Splits As splits
TreeNumber Unique integer indices for bifurcating tree topologies
SplitInformation Information content of a split
TreeShape Integer representing shape of a tree
TreeIsRooted Is tree rooted?
logDoubleFactorials Natural logarithms of double factorials
match.Splits Match splits
doubleFactorials Double factorials
in.Splits Splits in Splits object
Subtree Extract subtree
brewer Brewer palettes
TreesMatchingSplit Number of trees matching a bipartition split
as.Newick Write a phylogenetic tree in Newick format
TreeTools-package TreeTools: Create, Modify and Analyse Phylogenetic Trees
PhyToString phyDat to String
UnshiftTree Add Tree to Start of List
NRooted Number of rooted/unrooted trees
RandomTree Generate a random tree topology
SupportColour Support colour
TipLabels Extract tip labels
print.TreeNumber Print TreeNumber object
RootTree Root a phylogenetic tree
SampleOne Quick sample
AddTip Add a tip to a phylogenetic tree
CladeSizes Clade sizes
CollapseNode Collapse nodes on a phylogenetic tree
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License GPL (>= 3)
Copyright Incorporates C/C++ code from: ape by Emmanuel Paradis; phangorn by Klaus Scheip
SystemRequirements C++11
RdMacros Rdpack
LazyData true
ByteCompile true
Encoding UTF-8
Language en-GB
LinkingTo Rcpp
VignetteBuilder knitr
RoxygenNote 6.1.1
NeedsCompilation yes
Packaged 2019-12-19 17:20:16 UTC; ms609
Repository CRAN
Date/Publication 2019-12-19 18:20:07 UTC

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