A B C D E F G H I K L M N O P R S T U V W Y Z misc
ape-package | Analyses of Phylogenetics and Evolution |
$.multiPhylo | Compact Display of a Phylogeny |
ace | Ancestral Character Estimation |
add.scale.bar | Add a Scale Bar to a Phylogeny Plot |
AIC.ace | Ancestral Character Estimation |
AIC.phylo | Estimating Phylogenies by Maximum Likelihood |
all.equal.phylo | Global Comparison of two Phylogenies |
anova.ace | Ancestral Character Estimation |
ape | Analyses of Phylogenetics and Evolution |
as.alignment | Conversion Among DNA Sequence Internal Formats |
as.character.DNAbin | Conversion Among DNA Sequence Internal Formats |
as.DNAbin | Conversion Among DNA Sequence Internal Formats |
as.hclust.phylo | Conversion Among Tree Objects |
as.matching | Conversion Between Phylo and Matching Objects |
as.matrix.DNAbin | Manipulate DNA Sequences in Bit-Level Format |
as.phylo | Conversion Among Tree Objects |
as.phylo.formula | Conversion from Taxonomy Variables to Phylogenetic Trees |
as.phylo.hclust | Conversion Among Tree Objects |
as.phylo.matching | Conversion Between Phylo and Matching Objects |
as.phylo.phylog | Conversion Among Tree Objects |
axisPhylo | Axis on Side of Phylogeny |
balance | Balance of a Dichotomous Phylogenetic Tree |
base.freq | Base frequencies from DNA Sequences |
bd.ext | Extended Version of the Birth-Death Models to Estimate Speciation and Extinction Rates |
bind.tree | Binds Trees |
bionj | Tree Estimation Based on an Improved Version of the NJ Algorithm |
bird.families | Phylogeny of the Families of Birds From Sibley and Ahlquist |
bird.orders | Phylogeny of the Orders of Birds From Sibley and Ahlquist |
birthdeath | Estimation of Speciation and Extinction Rates With Birth-Death Models |
boot.phylo | Tree Bipartition and Bootstrapping Phylogenies |
branching.times | Branching Times of a Phylogenetic Tree |
CADM.global | Congruence among distance matrices |
CADM.post | Congruence among distance matrices |
carnivora | Carnivora body sizes and life history traits |
cbind.DNAbin | Manipulate DNA Sequences in Bit-Level Format |
cherry | Number of Cherries and Null Models of Trees |
chiroptera | Bat Phylogeny |
chronogram | Chronogram Computed by Nonparametric Rate Smoothing |
chronoMPL | Molecular Dating With Mean Path Lengths |
chronopl | Molecular Dating With Penalized Likelihood |
coalescent.intervals | Coalescent Intervals |
coef.corBlomberg | Blomberg et al.'s Correlation Structure |
coef.corBrownian | Brownian Correlation Structure |
coef.corGrafen | Grafen's (1989) Correlation Structure |
coef.corMartins | Martins's (1997) Correlation Structure |
coef.corPagel | Pagel's “lambda” Correlation Structure |
collapse.singles | Collapse Single Nodes |
collapsed.intervals | Collapsed Coalescent Intervals |
compar.cheverud | Cheverud's Comparative Method |
compar.gee | Comparative Analysis with GEEs |
compar.lynch | Lynch's Comparative Method |
compar.ou | Ornstein-Uhlenbeck Model for Continuous Characters |
compute.brlen | Branch Lengths Computation |
consensus | Concensus Trees |
cophenetic.phylo | Pairwise Distances from a Phylogenetic Tree |
cophyloplot | Plots two phylogenetic trees face to face with links between the tips. |
corBlomberg | Blomberg et al.'s Correlation Structure |
corBrownian | Brownian Correlation Structure |
corClasses | Phylogenetic Correlation Structures |
corGrafen | Grafen's (1989) Correlation Structure |
corMartins | Martins's (1997) Correlation Structure |
corMatrix.corBlomberg | Blomberg et al.'s Correlation Structure |
corMatrix.corBrownian | Brownian Correlation Structure |
corMatrix.corGrafen | Grafen's (1989) Correlation Structure |
corMatrix.corMartins | Martins's (1997) Correlation Structure |
corMatrix.corPagel | Pagel's “lambda” Correlation Structure |
corPagel | Pagel's “lambda” Correlation Structure |
corPhyl | Phylogenetic Correlation Structures |
correlogram.formula | Phylogenetic Correlogram |
cynipids | NEXUS Data Example |
data.nex | NEXUS Data Example |
del.gaps | Delete Alignment Gaps in DNA Sequences |
deviance.ace | Ancestral Character Estimation |
deviance.phylo | Estimating Phylogenies by Maximum Likelihood |
di2multi | Collapse and Resolve Multichotomies |
dist.dna | Pairwise Distances from DNA Sequences |
dist.gene | Pairwise Distances from Genetic Data |
dist.nodes | Pairwise Distances from a Phylogenetic Tree |
dist.topo | Topological Distances Between Two Trees |
diversi.gof | Tests of Constant Diversification Rates |
diversi.time | Analysis of Diversification with Survival Models |
DNAbin | Manipulate DNA Sequences in Bit-Level Format |
DNAmodel | Defines Models of DNA Evolution |
drop.tip | Remove Tips in a Phylogenetic Tree |
drop1.compar.gee | Comparative Analysis with GEEs |
edgelabels | Labelling the Nodes, Tips, and Edges of a Tree |
evolve.phylo | Ancestral Character Simulation |
extract.clade | Remove Tips in a Phylogenetic Tree |
extract.popsize | Reversible Jump MCMC to Infer Demographic History |
fastme | Tree Estimation Based on the Minimum Evolution Algorithm |
find.skyline.epsilon | Skyline Plot Estimate of Effective Population Size |
gammaStat | Gamma-Statistic of Pybus and Harvey |
GC.content | Content in GC from DNA Sequences |
H | Heterozygosity at a Locus Using Gene Frequencies |
heterozygosity | Heterozygosity at a Locus Using Gene Frequencies |
hivtree | Phylogenetic Tree of 193 HIV-1 Sequences |
howmanytrees | Calculate Numbers of Phylogenetic Trees |
identify.phylo | Graphical Identification of Nodes and Tips |
Initialize.corPhyl | Initialize a 'corPhyl' Structure Object |
is.binary.tree | Test for Binary Tree |
is.rooted | Roots Phylogenetic Trees |
is.ultrametric | Test if a Tree is Ultrametric |
klastorin | Klastorin's (1982) method for classifying genes as suggested by Misawa and Tajima (2000) |
ladderize | Ladderize a Tree |
landplants | Gene Tree of 36 Landplant rbcL Sequences |
lines.popsize | Reversible Jump MCMC to Infer Demographic History |
lines.skyline | Drawing Skyline Plot Graphs |
logLik.ace | Ancestral Character Estimation |
logLik.phylo | Estimating Phylogenies by Maximum Likelihood |
ltt.lines | Lineages Through Time Plot |
ltt.plot | Lineages Through Time Plot |
makeLabel | Label Management |
makeNodeLabel | Makes Node Labels |
mantel.test | Mantel Test for Similarity of Two Matrices |
mat3 | Three Matrices |
mat5M3ID | Five Trees |
mat5Mrand | Five Independent Trees |
matexpo | Matrix Exponential |
mcmc.popsize | Reversible Jump MCMC to Infer Demographic History |
mlphylo | Estimating Phylogenies by Maximum Likelihood |
mltt.plot | Lineages Through Time Plot |
Moran.I | Moran's I Autocorrelation Index |
mrca | Find Most Recent Common Ancestors Between Pairs |
mst | Minimum Spanning Tree |
multi2di | Collapse and Resolve Multichotomies |
Nedge | Print Summary of a Phylogeny |
new2old.phylo | Conversion Among Tree Objects |
nj | Neighbor-Joining Tree Estimation |
Nnode | Print Summary of a Phylogeny |
node.depth | Depth of Nodes and Tips |
nodelabels | Labelling the Nodes, Tips, and Edges of a Tree |
NPRS.criterion | Objective Function Employed in Nonparametric Rate Smoothing |
Ntip | Print Summary of a Phylogeny |
nuc.div | Nucleotide Diversity |
old2new.phylo | Conversion Among Tree Objects |
opsin | Gene Tree of 32 opsin Sequences |
phymltest | Fits a Bunch of Models with PhyML |
pic | Phylogenetically Independent Contrasts |
plot.ancestral | Plot Ancestral Character Values on a Tree |
plot.correlogram | Plot a Correlogram |
plot.correlogramList | Plot a Correlogram |
plot.mst | Minimum Spanning Tree |
plot.multiPhylo | Plot Phylogenies |
plot.phylo | Plot Phylogenies |
plot.phymltest | Fits a Bunch of Models with PhyML |
plot.popsize | Reversible Jump MCMC to Infer Demographic History |
plot.prop.part | Tree Bipartition and Bootstrapping Phylogenies |
plot.skyline | Drawing Skyline Plot Graphs |
plot.varcomp | Plot Variance Components |
print.birthdeath | Estimation of Speciation and Extinction Rates With Birth-Death Models |
print.compar.gee | Comparative Analysis with GEEs |
print.DNAbin | Manipulate DNA Sequences in Bit-Level Format |
print.multiPhylo | Compact Display of a Phylogeny |
print.phylo | Compact Display of a Phylogeny |
print.phymltest | Fits a Bunch of Models with PhyML |
print.prop.part | Tree Bipartition and Bootstrapping Phylogenies |
prop.clades | Tree Bipartition and Bootstrapping Phylogenies |
prop.part | Tree Bipartition and Bootstrapping Phylogenies |
ratogram | Ratogram Computed by Nonparametric Rate Smoothing |
rbind.DNAbin | Manipulate DNA Sequences in Bit-Level Format |
rcoal | Generates Random Trees |
read.caic | Read Tree File in CAIC Format |
read.dna | Read DNA Sequences in a File |
read.GenBank | Read DNA Sequences from GenBank via Internet |
read.nexus | Read Tree File in Nexus Format |
read.nexus.data | Read Character Data In NEXUS Format |
read.tree | Read Tree File in Parenthetic Format |
reorder.phylo | Internal Reordering of Trees |
rmtree | Generates Random Trees |
root | Roots Phylogenetic Trees |
rotate | Swapping sister clades |
rtree | Generates Random Trees |
seg.sites | Find Segregating Sites in DNA Sequences |
sh.test | Shimodaira-Hasegawa Test |
skyline | Skyline Plot Estimate of Effective Population Size |
skylineplot | Drawing Skyline Plot Graphs |
str.multiPhylo | Compact Display of a Phylogeny |
subtreeplot | Zoom on a Portion of a Phylogeny by Successive Clicks |
subtrees | All subtrees of a Phylogenetic Tree |
summary.DNAbin | Manipulate DNA Sequences in Bit-Level Format |
summary.phylo | Print Summary of a Phylogeny |
summary.phymltest | Fits a Bunch of Models with PhyML |
summary.prop.part | Tree Bipartition and Bootstrapping Phylogenies |
theta.h | Population Parameter THETA using Homozygosity |
theta.k | Population Parameter THETA using Expected Number of Alleles |
theta.s | Population Parameter THETA using Segregating Sites in DNA Sequences |
tiplabels | Labelling the Nodes, Tips, and Edges of a Tree |
unique.multiPhylo | Revomes Duplicate Trees |
unroot | Roots Phylogenetic Trees |
varcomp | Compute Variance Component Estimates |
vcv.phylo | Phylogenetic Variance-covariance or Correlation Matrix |
weight.taxo | Define Similarity Matrix |
weight.taxo2 | Define Similarity Matrix |
which.edge | Identifies Edges of a Tree |
woodmouse | Cytochrome b Gene Sequences of Woodmice |
write.dna | Write DNA Sequences in a File |
write.nexus | Write Tree File in Nexus Format |
write.nexus.data | Write Character Data In NEXUS Format |
write.tree | Write Tree File in Parenthetic Format |
yule | Fits Yule Model to a Phylogenetic Tree |
yule.cov | Fits the Yule Model With Covariates |
yule.time | Fits the Time-Dependent Yule Model |
zoom | Zoom on a Portion of a Phylogeny |
[.DNAbin | Manipulate DNA Sequences in Bit-Level Format |
[.multiPhylo | Compact Display of a Phylogeny |
[[.multiPhylo | Compact Display of a Phylogeny |