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1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 | CI Consistency Index and Retention Index
Laurasiatherian Laurasiatherian data (AWCMEE)
NJ Neighbor-Joining
SH.test Shimodaira-Hasegawa Test
SOWH.test Swofford-Olsen-Waddell-Hillis Test
add.tips Add tips to a tree
allSplits Splits representation of graphs and trees.
allTrees Compute all trees topologies.
ancestral.pml Ancestral character reconstruction.
as.networx Phylogenetic networks
bab Branch and bound for finding all most
parsimonious trees
bootstrap.pml Bootstrap
chloroplast Chloroplast alignment
cladePar Utility function to plot.phylo
coalSpeciesTree Species Tree
consensusNet Computes a consensusNetwork from a list of
trees Computes a 'networx' object from a
collection of splits.
cophenetic.networx Pairwise Distances from a Phylogenetic Network
createLabel Compare splits and add support values to an
object
delta.score Computes the delta score
densiTree Plots a densiTree.
designTree Compute a design matrix or non-negative LS
discrete.gamma Internal maximum likelihood functions.
dist.hamming Pairwise Distances from Sequences
dist.p Pairwise Polymorphism P-Distances from DNA
Sequences
distanceHadamard Distance Hadamard
fitch Parsimony tree.
getClans Clans, slices and clips
getRoot Tree manipulation
hadamard Hadamard Matrices and Fast Hadamard
Multiplication
identify.networx Identify splits in a network
ldfactorial Arithmetic Operators
lento Lento plot
mast Maximum agreement subtree
maxCladeCred Maximum clade credibility tree
modelTest ModelTest
multiphyDat2pmlPart Partition model.
neighborNet Computes a neighborNet from a distance matrix
nni Tree rearrangements.
phangorn-package Phylogenetic analysis in R
phyDat Conversion among Sequence Formats
pml.control Likelihood of a tree.
pmlCluster Stochastic Partitioning
pmlMix Phylogenetic mixture model
read.aa Read Amino Acid Sequences in a File
read.nexus.splits Function to import and export splits and
networks
simSeq Simulate sequences.
splitsNetwork Phylogenetic Network
superTree Super Tree methods
treedist Distances between trees
upgma UPGMA and WPGMA
writeDist Writing and reading distances in phylip and
nexus format
yeast Yeast alignment (Rokas et al.)
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