Entry: Correlogram
Aliases: Correlogram correlogram.formula correlogram.phylo
Keywords: regression dplot
Description: Compute a correlogram
URL: ../../../library/ape/html/Correlogram.html

Entry: GC.content
Aliases: GC.content
Keywords: univar
Description: Content in GC from DNA Sequences
URL: ../../../library/ape/html/GC.content.html

Entry: Initialize.corPhyl
Aliases: Initialize.corPhyl
Keywords: models manip
Description: Initialize a 'corPhyl' Structure Object
URL: ../../../library/ape/html/Initialize.corPhyl.html

Entry: Moran.I
Aliases: Moran.I
Keywords: models regression
Description: Moran's I Autocorrelation Index
URL: ../../../library/ape/html/MoranI.html

Entry: NPRS.criterion
Aliases: NPRS.criterion
Keywords: manip
Description: Objective Function Employed in Nonparametric Rate Smoothing
URL: ../../../library/ape/html/NPRS.criterion.html

Entry: add.scale.bar
Aliases: add.scale.bar
Keywords: aplot
Description: Add a Scale Bar to a Phylogeny Plot
URL: ../../../library/ape/html/add.scale.bar.html

Entry: all.equal.phylo
Aliases: all.equal.phylo
Keywords: manip
Description: Global Comparison of two Phylogenies
URL: ../../../library/ape/html/all.equal.phylo.html

Entry: ape-internal
Aliases: tree.build f.cherry.yule f.cherry.uniform sort.index nsca get.dna perm.rowscols mant.zstat lower.triang clado.build getDurations getEdgeLengths getExternalParams getNEdges getNFreeParams getRates objFuncLogScale optimTree phylogram prepareTree setTree buildTreeFromPhylo destroyTree getError nEdges nNodes nTips getMisawaTajima phylogram.plot cladogram.plot unrooted.plot unrooted.xy node.height node.height.clado birth.step death.step ht.move loglik.pop pos.move
Keywords: internal
Description: Internal Ape Functions
URL: ../../../library/ape/html/ape-internal.html

Entry: as.phylo
Aliases: as.phylo as.phylo.hclust as.phylo.phylog as.hclust.phylo
Keywords: manip
Description: Conversion Among Tree Objects
URL: ../../../library/ape/html/as.phylo.html

Entry: axisPhylo
Aliases: axisPhylo
Keywords: aplot
Description: Axis on Side of Phylogeny
URL: ../../../library/ape/html/axisPhylo.html

Entry: balance
Aliases: balance
Keywords: manip
Description: Balance of a Dichotomous Phylogenetic Tree
URL: ../../../library/ape/html/balance.html

Entry: base.freq
Aliases: base.freq
Keywords: univar
Description: Base frequencies from DNA Sequences
URL: ../../../library/ape/html/base.freq.html

Entry: bd.ext
Aliases: bd.ext
Keywords: models
Description: Extended Version of the Birth-Death Models to Estimate Speciation and Extinction Rates
URL: ../../../library/ape/html/bd.ext.html

Entry: bind.tree
Aliases: bind.tree
Keywords: manip
Description: Binds Trees
URL: ../../../library/ape/html/bind.tree.html

Entry: bird.families
Aliases: bird.families
Keywords: datasets
Description: Phylogeny of the Families of Birds From Sibley and Ahlquist
URL: ../../../library/ape/html/bird.families.html

Entry: bird.orders
Aliases: bird.orders
Keywords: datasets
Description: Phylogeny of the Orders of Birds From Sibley and Ahlquist
URL: ../../../library/ape/html/bird.orders.html

Entry: birthdeath
Aliases: birthdeath
Keywords: models
Description: Estimation of Speciation and Extinction Rates With Birth-Death Models
URL: ../../../library/ape/html/birthdeath.html

Entry: branching.times
Aliases: branching.times
Keywords: manip
Description: Branching Times of a Phylogenetic Tree
URL: ../../../library/ape/html/branching.times.html

Entry: carnivora
Aliases: carnivora
Keywords: datasets
Description: Carnivora body sizes and life history traits
URL: ../../../library/ape/html/carnivora.html

Entry: cherry
Aliases: cherry
Keywords: univar
Description: Number of Cherries and Null Models of Trees
URL: ../../../library/ape/html/cherry.html

Entry: chiroptera
Aliases: chiroptera
Keywords: datasets
Description: Bat Phylogeny
URL: ../../../library/ape/html/chiroptera.html

Entry: chronogram
Aliases: chronogram
Keywords: manip
Description: Chronogram Computed by Nonparametric Rate Smoothing
URL: ../../../library/ape/html/chronogram.html

Entry: coalescent.intervals
Aliases: coalescent.intervals coalescent.intervals.phylo coalescent.intervals.default
Keywords: manip
Description: Coalescent Intervals
URL: ../../../library/ape/html/coalescent.intervals.html

Entry: collapsed.intervals
Aliases: collapsed.intervals
Keywords: manip
Description: Collapsed Coalescent Intervals
URL: ../../../library/ape/html/collapsed.intervals.html

Entry: compar.cheverud
Aliases: compar.cheverud
Keywords: regression
Description: Cheverud's Comparative Method
URL: ../../../library/ape/html/compar.cheverud.html

Entry: compar.gee
Aliases: compar.gee print.compar.gee
Keywords: regression
Description: Comparative Analysis with GEEs
URL: ../../../library/ape/html/compar.gee.html

Entry: compar.lynch
Aliases: compar.lynch
Keywords: regression
Description: Lynch's Comparative Method
URL: ../../../library/ape/html/compar.lynch.html

Entry: compute.brlen
Aliases: compute.brlen
Keywords: manip
Description: Branch lengths Computation
URL: ../../../library/ape/html/compute.brlen.html

Entry: corBrownian
Aliases: corBrownian coef.corBrownian corMatrix.corBrownian
Keywords: models
Description: Brownian Correlation Structure
URL: ../../../library/ape/html/corBrownian.html

Entry: corClasses
Aliases: corClasses corPhyl
Keywords: models
Description: Phylogenetic Correlation Structures
URL: ../../../library/ape/html/corClasses.html

Entry: corGrafen
Aliases: corGrafen coef.corGrafen corMatrix.corGrafen
Keywords: models
Description: Grafen's (1989) Correlation Structure
URL: ../../../library/ape/html/corGrafen.html

Entry: corMartins
Aliases: corMartins coef.corMartins corMatrix.corMartins
Keywords: models
Description: Martins's (1997) Correlation Structure
URL: ../../../library/ape/html/corMartins.html

Entry: discrete.dist
Aliases: discrete.dist
Keywords: regression manip
Description: Taxonomic Level from a Pairwise Distances Matrix
URL: ../../../library/ape/html/discrete.dist.html

Entry: dist.dna
Aliases: dist.dna dist.dna.JukesCantor dist.dna.TajimaNei dist.dna.Kimura dist.dna.Tamura dist.dna.TamuraNei
Keywords: manip multivariate
Description: Pairwise Distances from DNA Sequences
URL: ../../../library/ape/html/dist.dna.html

Entry: dist.gene
Aliases: dist.gene dist.gene.pairwise dist.gene.percentage
Keywords: manip
Description: Pairwise Distances from Genetic Data
URL: ../../../library/ape/html/dist.gene.html

Entry: dist.phylo
Aliases: dist.phylo
Keywords: manip
Description: Pairwise Distances from a Phylogenetic Tree
URL: ../../../library/ape/html/dist.phylo.html

Entry: dist.taxo
Aliases: dist.taxo
Keywords: regression manip
Description: Pairwise Distances from a Taxonomic Level
URL: ../../../library/ape/html/dist.taxo.html

Entry: diversi.gof
Aliases: diversi.gof
Keywords: univar
Description: Tests of Constant Diversification Rates
URL: ../../../library/ape/html/diversi.gof.html

Entry: diversi.time
Aliases: diversi.time
Keywords: models
Description: Analysis of Diversification with Survival Models
URL: ../../../library/ape/html/diversi.time.html

Entry: drop.tip
Aliases: drop.tip
Keywords: manip
Description: Remove Tips in a Phylogenetic Tree
URL: ../../../library/ape/html/drop.tip.html

Entry: gammaStat
Aliases: gammaStat
Keywords: univar
Description: Gamma-Statistic of Pybus and Harvey
URL: ../../../library/ape/html/gammaStat.html

Entry: heterozygosity
Aliases: heterozygosity H
Keywords: manip univar
Description: Heterozygosity at a Locus Using Gene Frequencies
URL: ../../../library/ape/html/heterozygosity.html

Entry: hivtree
Aliases: hivtree hivtree.newick hivtree.table
Keywords: datasets
Description: Phylogenetic Tree of 193 HIV-1 Sequences
URL: ../../../library/ape/html/hivtree.html

Entry: howmanytrees
Aliases: howmanytrees
Keywords: arith math
Description: Calculate Numbers of Phylogenetic Trees
URL: ../../../library/ape/html/howmanytrees.html

Entry: is.binary.tree
Aliases: is.binary.tree
Keywords: logic
Description: Test for Binary Tree
URL: ../../../library/ape/html/is.binary.tree.html

Entry: is.ultrametric
Aliases: is.ultrametric
Keywords: utilities
Description: Test if a Tree is Ultrametric
URL: ../../../library/ape/html/is.ultrametric.html

Entry: klastorin
Aliases: klastorin
Keywords: manip
Description: Klastorin's (1982) method for classifying genes as suggested by Misawa and Tajima (2000)
URL: ../../../library/ape/html/klastorin.html

Entry: landplants
Aliases: landplants landplants.newick
Keywords: datasets
Description: Gene Tree of 36 Landplant rbcL Sequences
URL: ../../../library/ape/html/landplants.html

Entry: ltt.plot
Aliases: ltt.plot ltt.lines mltt.plot
Keywords: hplot aplot
Description: Lineages Through Time Plot
URL: ../../../library/ape/html/ltt.plot.html

Entry: mantel.test
Aliases: mantel.test
Keywords: multivariate
Description: Mantel Test for Similarity of Two Matrices
URL: ../../../library/ape/html/mantel.test.html

Entry: mcmc.popsize
Aliases: mcmc.popsize extract.popsize plot.popsize lines.popsize
Keywords: manip
Description: Reversible Jump MCMC to Infer Demographic History
URL: ../../../library/ape/html/mcmc.popsize.html

Entry: mst
Aliases: mst plot.mst
Keywords: multivariate
Description: Minimum Spanning Tree
URL: ../../../library/ape/html/mst.html

Entry: nj
Aliases: nj
Keywords: models
Description: Neighbor-Joining Tree Estimation
URL: ../../../library/ape/html/nj.html

Entry: node.depth
Aliases: node.depth
Keywords: manip
Description: Depth of Nodes and Tips
URL: ../../../library/ape/html/node.depth.html

Entry: node.leafnumber
Aliases: node.leafnumber
Keywords: manip
Description: Get the Number of Leaves for a Node
URL: ../../../library/ape/html/node.leafnumber.html

Entry: node.sons
Aliases: node.sons
Keywords: manip
Description: Get the list of Sons for a Node
URL: ../../../library/ape/html/node.sons.html

Entry: nodelabels
Aliases: nodelabels
Keywords: aplot
Description: Labelling the Nodes of a Tree
URL: ../../../library/ape/html/nodelabels.html

Entry: opsin
Aliases: opsin opsin.newick
Keywords: datasets
Description: Gene Tree of 32 opsin Sequences
URL: ../../../library/ape/html/opsin.html

Entry: panel.superpose.correlogram
Aliases: panel.superpose.correlogram
Keywords: dplot
Description: Lattice panel used in 'plot.correlogramList'.
URL: ../../../library/ape/html/panel.superpose.correlogram.html

Entry: phymltest
Aliases: phymltest print.phymltest summary.phymltest plot.phymltest
Keywords: models
Description: Fits a Bunch of Models with PHYML
URL: ../../../library/ape/html/phymltest.html

Entry: pic
Aliases: pic
Keywords: regression
Description: Phylogenetically Independent Contrasts
URL: ../../../library/ape/html/pic.html

Entry: plot.correlogram
Aliases: plot.correlogram
Keywords: hplot
Description: Plot a Correlogram
URL: ../../../library/ape/html/plot.correlogram.html

Entry: plot.correlogramList
Aliases: plot.correlogramList
Keywords: hplot
Description: Plot several Correlograms
URL: ../../../library/ape/html/plot.correlogramList.html

Entry: plot.phylo
Aliases: plot.phylo
Keywords: hplot
Description: Plot Phylogenies
URL: ../../../library/ape/html/plot.phylo.html

Entry: plot.varcomp
Aliases: plot.varcomp
Keywords: hplot
Description: Plot Variance Components
URL: ../../../library/ape/html/plot.varcomp.html

Entry: ratogram
Aliases: ratogram
Keywords: manip
Description: Ratogram Computed by Nonparametric Rate Smoothing
URL: ../../../library/ape/html/ratogram.html

Entry: read.GenBank
Aliases: read.GenBank
Keywords: IO
Description: Read DNA Sequences from GenBank via Internet
URL: ../../../library/ape/html/read.GenBank.html

Entry: read.dna
Aliases: read.dna
Keywords: IO
Description: Read DNA Sequences in a File
URL: ../../../library/ape/html/read.dna.html

Entry: read.nexus
Aliases: read.nexus
Keywords: manip IO
Description: Read Tree File in Nexus Format
URL: ../../../library/ape/html/read.nexus.html

Entry: read.tree
Aliases: read.tree
Keywords: manip IO
Description: Read Tree File in Parenthetic Format
URL: ../../../library/ape/html/read.tree.html

Entry: root
Aliases: root
Keywords: manip
Description: Roots Phylogenetic Trees
URL: ../../../library/ape/html/root.html

Entry: rotate
Aliases: rotate
Keywords: manip
Description: Rotate an Internal Branch of a Tree
URL: ../../../library/ape/html/rotate.html

Entry: rtree
Aliases: rtree
Keywords: datagen
Description: Generates Random Trees
URL: ../../../library/ape/html/rtree.html

Entry: seg.sites
Aliases: seg.sites
Keywords: univar
Description: Find Segregating Sites in DNA Sequences
URL: ../../../library/ape/html/seg.sites.html

Entry: skyline
Aliases: skyline skyline.phylo skyline.coalescentIntervals skyline.collapsedIntervals find.skyline.epsilon
Keywords: manip
Description: Skyline Plot Estimate of Effective Population Size
URL: ../../../library/ape/html/skyline.html

Entry: skylineplot
Aliases: skylineplot plot.skyline lines.skyline skylineplot.deluxe
Keywords: hplot
Description: Drawing Skyline Plot Graphs
URL: ../../../library/ape/html/skylineplot.html

Entry: summary.phylo
Aliases: summary.phylo
Keywords: manip
Description: Print Summary of a Phylogeny
URL: ../../../library/ape/html/summary.phylo.html

Entry: theta.h
Aliases: theta.h
Keywords: manip univar
Description: Population Parameter THETA using Homozygosity
URL: ../../../library/ape/html/theta.h.html

Entry: theta.k
Aliases: theta.k
Keywords: manip univar
Description: Population Parameter THETA using Expected Number of Alleles
URL: ../../../library/ape/html/theta.k.html

Entry: theta.s
Aliases: theta.s
Keywords: manip univar
Description: Population Parameter THETA using Segregating Sites in DNA Sequences
URL: ../../../library/ape/html/theta.s.html

Entry: varcomp
Aliases: varcomp
Keywords: regression dplot
Description: Compute Variance Component Estimates
URL: ../../../library/ape/html/varcomp.html

Entry: vcv.phylo
Aliases: vcv.phylo
Keywords: manip multivariate
Description: Phylogenetic Variance-covariance or Correlation Matrix
URL: ../../../library/ape/html/vcv.phylo.html

Entry: which.edge
Aliases: which.edge
Keywords: manip
Description: Identifies Edges of a Tree
URL: ../../../library/ape/html/which.edge.html

Entry: woodmouse
Aliases: woodmouse
Keywords: datasets
Description: Cytochrome b Gene Sequences of Woodmice
URL: ../../../library/ape/html/woodmouse.html

Entry: write.dna
Aliases: write.dna
Keywords: IO
Description: Write DNA Sequences in a File
URL: ../../../library/ape/html/write.dna.html

Entry: write.nexus
Aliases: write.nexus
Keywords: manip IO
Description: Write Tree File in Nexus Format
URL: ../../../library/ape/html/write.nexus.html

Entry: write.tree
Aliases: write.tree
Keywords: manip IO
Description: Write Tree File in Parenthetic Format
URL: ../../../library/ape/html/write.tree.html

Entry: xenarthra
Aliases: xenarthra
Keywords: datasets
Description: Molecular Phylogeny of Living Xenarthrans
URL: ../../../library/ape/html/xenarthra.html

Entry: yule
Aliases: yule
Keywords: models
Description: Fits Yule Model to a Phylogenetic Tree
URL: ../../../library/ape/html/yule.html

Entry: yule.cov
Aliases: yule.cov
Keywords: models
Description: Fits the Yule Model With Covariates
URL: ../../../library/ape/html/yule.cov.html

Entry: zoom
Aliases: zoom
Keywords: hplot
Description: Zoom on a Portion of a Phylogeny
URL: ../../../library/ape/html/zoom.html
