axisPhylo |
Axis on Side of Phylogeny |
dnds |
dN/dS Ratio |
alview |
Print DNA or AA Sequence Alignement |
all.equal.phylo |
Global Comparison of two Phylogenies |
dbd |
Probability Density Under Birth--Death Models |
comparePhylo |
Compare Two "phylo" Objects |
cophyloplot |
Plots two phylogenetic trees face to face with links between the tips. |
compar.ou |
Ornstein--Uhlenbeck Model for Continuous Characters |
corBlomberg |
Blomberg et al.'s Correlation Structure |
def |
Definition of Vectors for Plotting or Annotating |
add.scale.bar |
Add a Scale Bar to a Phylogeny Plot |
Moran.I |
Moran's I Autocorrelation Index |
alex |
Alignment Explorer With Multiple Devices |
ape-package |
Analyses of Phylogenetics and Evolution |
ape-internal |
Internal Ape Functions |
bd.ext |
Extended Version of the Birth-Death Models to Estimate Speciation
and Extinction Rates |
base.freq |
Base frequencies from DNA Sequences |
branching.times |
Branching Times of a Phylogenetic Tree |
c.phylo |
Building Lists of Trees |
drop.tip |
Remove Tips in a Phylogenetic Tree |
balance |
Balance of a Dichotomous Phylogenetic Tree |
bird.families |
Phylogeny of the Families of Birds From Sibley and Ahlquist |
kronoviz |
Plot Multiple Chronograms on the Same Scale |
mantel.test |
Mantel Test for Similarity of Two Matrices |
is.ultrametric |
Test if a Tree is Ultrametric |
bird.orders |
Phylogeny of the Orders of Birds From Sibley and Ahlquist |
as.phylo |
Conversion Among Tree and Network Objects |
apetools |
Tools to Explore Files |
as.alignment |
Conversion Among DNA Sequence Internal Formats |
mat3 |
Three Matrices |
additive |
Incomplete Distance Matrix Filling |
coalescent.intervals |
Coalescent Intervals |
all.equal.DNAbin |
Compare DNA Sets |
bd.time |
Time-Dependent Birth-Death Models |
collapse.singles |
Collapse Single Nodes |
as.bitsplits |
Split Frequencies and Conversion Among Split Classes |
compar.gee |
Comparative Analysis with GEEs |
phydataplot |
Tree Annotation |
print.phylo |
Compact Display of a Phylogeny |
pcoa |
Principal Coordinate Analysis |
as.phylo.formula |
Conversion from Taxonomy Variables to Phylogenetic Trees |
compar.lynch |
Lynch's Comparative Method |
binaryPGLMM |
Phylogenetic Generalized Linear Mixed Model for Binary Data |
checkAlignment |
Check DNA Alignments |
as.matching |
Conversion Between Phylo and Matching Objects |
carnivora |
Carnivora body sizes and life history traits |
rDNAbin |
Random DNA Sequences |
birthdeath |
Estimation of Speciation and Extinction Rates With Birth-Death Models |
read.gff |
Read GFF Files |
read.nexus |
Read Tree File in Nexus Format |
boot.phylo |
Tree Bipartition and Bootstrapping Phylogenies |
bind.tree |
Binds Trees |
checkLabel |
Checking Labels |
woodmouse |
Cytochrome b Gene Sequences of Woodmice |
chronopl |
Molecular Dating With Penalized Likelihood |
chronoMPL |
Molecular Dating With Mean Path Lengths |
checkValidPhylo |
Check the Structure of a "phylo" Object |
BIONJ |
Tree Estimation Based on an Improved Version of the NJ Algorithm |
chronos |
Molecular Dating by Penalised Likelihood and Maximum Likelihood |
consensus |
Concensus Trees |
write.dna |
Write DNA Sequences in a File |
cherry |
Number of Cherries and Null Models of Trees |
corPagel |
Pagel's ``lambda'' Correlation Structure |
chiroptera |
Bat Phylogeny |
delta.plot |
Delta Plots |
del.gaps |
Delete Alignment Gaps in DNA Sequences |
corphylo |
Correlations among Multiple Traits with Phylogenetic Signal |
cophenetic.phylo |
Pairwise Distances from a Phylogenetic Tree |
dist.dna |
Pairwise Distances from DNA Sequences |
corBrownian |
Brownian Correlation Structure |
compute.brlen |
Branch Lengths Computation |
howmanytrees |
Calculate Numbers of Phylogenetic Trees |
corClasses |
Phylogenetic Correlation Structures |
identify.phylo |
Graphical Identification of Nodes and Tips |
is.compatible |
Check Compatibility of Splits |
is.monophyletic |
Is Group Monophyletic |
makeLabel |
Label Management |
compute.brtime |
Compute and Set Branching Times |
clustal |
Multiple Sequence Alignment with External Applications |
makeNodeLabel |
Makes Node Labels |
dist.gene |
Pairwise Distances from Genetic Data |
gammaStat |
Gamma-Statistic of Pybus and Harvey |
correlogram.formula |
Phylogenetic Correlogram |
hivtree |
Phylogenetic Tree of 193 HIV-1 Sequences |
collapsed.intervals |
Collapsed Coalescent Intervals |
compar.cheverud |
Cheverud's Comparative Method |
corGrafen |
Grafen's (1989) Correlation Structure |
data.nex |
NEXUS Data Example |
label2table |
Label Management |
corMartins |
Martins's (1997) Correlation Structure |
dist.topo |
Topological Distances Between Two Trees |
diversi.time |
Analysis of Diversification with Survival Models |
diversity.contrast.test |
Diversity Contrast Test |
diversi.gof |
Tests of Constant Diversification Rates |
ladderize |
Ladderize a Tree |
edges |
Draw Additional Edges on a Plotted Tree |
image.DNAbin |
Plot of DNA Sequence Alignement |
evonet |
Evolutionary Networks |
njs |
Tree Reconstruction from Incomplete Distances With NJ* or bio-NJ* |
matexpo |
Matrix Exponential |
ewLasso |
Incomplete distances and edge weights of unrooted topology |
is.binary |
Test for Binary Tree |
mcmc.popsize |
Reversible Jump MCMC to Infer Demographic History |
FastME |
Tree Estimation Based on the Minimum Evolution Algorithm |
node.dating |
node.dating |
lmorigin |
Multiple regression through the origin |
mcconwaysims.test |
McConway-Sims Test of Homogeneous Diversification |
node.depth |
Depth and Heights of Nodes and Tips |
pic.ortho |
Phylogenetically Independent Orthonormal Contrasts |
plot.correlogram |
Plot a Correlogram |
rTraitMult |
Multivariate Character Simulation |
mrca |
Find Most Recent Common Ancestors Between Pairs |
mst |
Minimum Spanning Tree |
ltt.plot |
Lineages Through Time Plot |
read.GenBank |
Read DNA Sequences from GenBank via Internet |
mixedFontLabel |
Mixed Font Labels for Plotting |
nodelabels |
Labelling the Nodes, Tips, and Edges of a Tree |
nodepath |
Find Paths of Nodes |
phymltest |
Fits a Bunch of Models with PhyML |
mat5M3ID |
Five Trees |
pic |
Phylogenetically Independent Contrasts |
plot.varcomp |
Plot Variance Components |
parafit |
Test of host-parasite coevolution |
multi2di |
Collapse and Resolve Multichotomies |
rTraitCont |
Continuous Character Simulation |
reconstruct |
Continuous Ancestral Character Estimation |
mat5Mrand |
Five Independent Trees |
mvr |
Minimum Variance Reduction |
plotTreeTime |
Plot Tree With Time Axis |
read.nexus.data |
Read Character Data In NEXUS Format |
reorder.phylo |
Internal Reordering of Trees |
multiphylo |
Manipulating Lists of Trees |
rTraitDisc |
Discrete Character Simulation |
nj |
Neighbor-Joining Tree Estimation |
root |
Roots Phylogenetic Trees |
plot.phylo |
Plot Phylogenies |
plot.phylo.extra |
Extra Fuctions to Plot and Annotate Phylogenies |
read.caic |
Read Tree File in CAIC Format |
read.tree |
Read Tree File in Parenthetic Format |
speciesTree |
Species Tree Estimation |
subtreeplot |
Zoom on a Portion of a Phylogeny by Successive Clicks |
stree |
Generates Systematic Regular Trees |
subtrees |
All subtrees of a Phylogenetic Tree |
rtree |
Generates Random Trees |
rotate |
Swapping Sister Clades |
triangMtd |
Tree Reconstruction Based on the Triangles Method |
seg.sites |
Find Segregating Sites in DNA Sequences |
rtt |
Root a Tree by Root-to-Tip Regression |
skyline |
Skyline Plot Estimate of Effective Population Size |
treePop |
Tree Popping |
trex |
Tree Explorer With Multiple Devices |
read.dna |
Read DNA Sequences in a File |
summary.phylo |
Print Summary of a Phylogeny |
unique.multiPhylo |
Revomes Duplicate Trees |
updateLabel |
Update Labels |
varCompPhylip |
Variance Components with Orthonormal Contrasts |
write.tree |
Write Tree File in Parenthetic Format |
yule |
Fits the Yule Model to a Phylogenetic Tree |
yule.cov |
Fits the Yule Model With Covariates |
trans |
Translation from DNA to Amino Acid Sequences |
richness.yule.test |
Test of Diversification-Shift With the Yule Process |
yule.time |
Fits the Time-Dependent Yule Model |
rlineage |
Tree Simulation Under the Time-Dependent Birth--Death Models |
write.nexus |
Write Tree File in Nexus Format |
write.nexus.data |
Write Character Data in NEXUS Format |
vcv2phylo |
Variance-Covariance Matrix to Tree |
zoom |
Zoom on a Portion of a Phylogeny |
weight.taxo |
Define Similarity Matrix |
skylineplot |
Drawing Skyline Plot Graphs |
slowinskiguyer.test |
Slowinski-Guyer Test of Homogeneous Diversification |
varcomp |
Compute Variance Component Estimates |
vcv |
Phylogenetic Variance-covariance or Correlation Matrix |
where |
Find Patterns in DNA Sequences |
which.edge |
Identifies Edges of a Tree |
AAbin |
Amino Acid Sequences |
DNAbin2indel |
Recode Blocks of Indels |
Initialize.corPhyl |
Initialize a `corPhyl' Structure Object |
MPR |
Most Parsimonious Reconstruction |
DNAbin |
Manipulate DNA Sequences in Bit-Level Format |
SDM |
Construction of Consensus Distance Matrix With SDM |
LTT |
Theoretical Lineage-Through Time Plots |
ace |
Ancestral Character Estimation |
CADM.global |
Congruence among distance matrices |
No Results! |