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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 | Ancestors tree utility function
Laurasiatherian Laurasiatherian data (AWCMEE)
NJ Neighbor-Joining
SH.test Shimodaira-Hasegawa Test
SOWH.test Swofford-Olsen-Waddell-Hillis Test
allTrees Compute all trees topologies.
ancestral.pml Ancestral character reconstruction.
as.splits Splits representation of graphs and trees.
bab Branch and bound for finding all most
parsimonious trees
bootstrap.pml Bootstrap
chloroplast Chloroplast alignment
cladePar Utility function to plot.phylo
consensusNet Computes a consensusNetwork from a list of
trees Computes a 'networx' object from a
collection of splits.
densiTree Plots a densiTree.
designTree Compute a design matrix or non-negative LS
dfactorial Arithmetic Operators
dist.hamming Pairwise Distances from Sequences
dist.p Pairwise Polymorphism P-Distances from DNA
Sequences
distanceHadamard Distance Hadamard
getClans Clans, slices and clips
hadamard Hadamard Matrices and Fast Hadamard
Multiplication
lento Lento plot
midpoint Tree manipulation
modelTest ModelTest
neighborNet Computes a neighborNet from a distance matrix
nni Tree rearrangements.
parsimony Parsimony tree.
phangorn-package Phylogenetic analysis in R
phyDat Conversion among Sequence Formats
plot.networx Phylogenetic networks
pml Likelihood of a tree.
pml.fit Internal maximum likelihood functions.
pmlCluster Stochastic Partitioning
pmlMix Phylogenetic mixture model
pmlPart Partition model.
read.aa Read Amino Acid Sequences in a File
simSeq Simulate sequences.
splitsNetwork Phylogenetic Network
superTree Super Tree and Species Tree methods
treedist Distances between trees
upgma UPGMA and WPGMA
yeast Yeast alignment (Rokas et al.)
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