Files in ape

Analyses of Phylogenetics and Evolution

README.md R/RcppExports.R R/balance.R R/compar.ou.R R/compute.brtime.R R/mvr.R R/varcomp.R R/skyline.R R/ewLasso.R R/cophyloplot.R R/write.nexus.data.R R/DNA.R R/dist.gene.R R/plot.phylo.R R/ace.R R/Cheverud.R R/evonet.R R/speciesTree.R R/write.dna.R R/reorder.phylo.R R/plot.phyloExtra.R R/is.binary.tree.R R/pic.R R/triangMtd.R R/matexpo.R R/read.dna.R R/pcoa.R R/def.R R/drop.tip.R R/compar.lynch.R R/yule.R R/ladderize.R R/read.nexus.R R/dist.topo.R R/read.nexus.data.R R/rotate.R R/is.monophyletic.R R/as.phylo.formula.R R/yule.time.R R/extract.popsize.R R/makeNodeLabel.R R/diversi.time.R R/parafit.R R/rTrait.R R/rtree.R R/mcmc.popsize.R R/multi2di.R R/diversi.gof.R R/mantel.test.R R/gammaStat.R R/MPR.R R/nodepath.R R/print.parafit.R R/cherry.R R/mrca.R R/write.tree.R R/clustal.R R/is.compatible.R R/scales.R R/subtreeplot.R R/birthdeath.R R/reconstruct.R R/as.matching.R R/biplot.pcoa.R R/dbd.R R/binaryPGLMM.R R/collapsed.intervals.R R/comparePhylo.R R/makeLabel.R R/vcv2phylo.R R/cophenetic.phylo.R R/collapse.singles.R R/read.caic.R R/as.phylo.R R/MoranI.R R/rtt.R R/read.gff.R R/write.nexus.R R/plotPhyloCoor.R R/zoom.R R/read.GenBank.R R/delta.plot.R R/me.R R/lmorigin.R R/CDF.birth.death.R R/mst.R R/CADM.global.R R/PGLS.R R/which.edge.R R/is.ultrametric.R R/chronos.R R/unique.multiPhylo.R R/summary.phylo.R R/skylineplot.R R/bind.tree.R R/CADM.post.R R/corphylo.R R/plot.popsize.R R/alex.R R/SDM.R R/zzz.R R/checkValidPhylo.R R/phydataplot.R R/print.lmorigin.R R/read.tree.R R/additive.R R/branching.times.R R/SlowinskiGuyer.R R/root.R R/subtrees.R R/njs.R R/ltt.plot.R R/compar.gee.R R/as.bitsplits.R R/all.equal.phylo.R R/coalescent.intervals.R R/identify.phylo.R R/chronopl.R R/vcv.phylo.R R/node.dating.R R/apetools.R R/nodelabels.R R/phymltest.R R/treePop.R R/chronoMPL.R R/howmanytrees.R R/nj.R inst/doc/DrawingPhylogenies.R inst/doc/DrawingPhylogenies.pdf inst/doc/RandomTopologies.pdf inst/doc/MoranI.R inst/doc/MoranI.pdf inst/doc/RandomTopologies.R man/mantel.test.Rd man/speciesTree.Rd man/zoom.Rd man/corBrownian.Rd man/additive.Rd man/reorder.phylo.Rd man/plotTreeTime.Rd man/multi2di.Rd man/skylineplot.Rd man/weight.taxo.Rd man/matexpo.Rd man/checkValidPhylo.Rd man/compar.cheverud.Rd man/rotate.Rd man/dist.dna.Rd man/bd.time.Rd man/chronoMPL.Rd man/birthdeath.Rd man/evonet.Rd man/binaryPGLMM.Rd man/label2table.Rd man/print.phylo.Rd man/branching.times.Rd man/summary.phylo.Rd man/cophenetic.phylo.Rd man/nodepath.Rd man/add.scale.bar.Rd man/lmorigin.Rd man/node.depth.Rd man/ltt.plot.Rd man/mrca.Rd man/collapsed.intervals.Rd man/checkLabel.Rd man/mcmc.popsize.Rd man/stree.Rd man/boot.phylo.Rd man/triangMtd.Rd man/drop.tip.Rd man/corphylo.Rd man/is.ultrametric.Rd man/ape-package.Rd man/makeLabel.Rd man/alview.Rd man/rlineage.Rd man/rtree.Rd man/corGrafen.Rd man/axisPhylo.Rd man/collapse.singles.Rd man/read.caic.Rd man/DNAbin2indel.Rd man/cophyloplot.Rd man/root.Rd man/read.gff.Rd man/hivtree.Rd man/nj.Rd man/all.equal.DNAbin.Rd man/skyline.Rd man/subtreeplot.Rd man/dnds.Rd man/bionj.Rd man/dist.topo.Rd man/write.dna.Rd man/woodmouse.Rd man/base.freq.Rd man/compute.brlen.Rd man/dbd.Rd man/DNAbin.Rd man/trans.Rd man/c.phylo.Rd man/SDM.Rd man/solveAmbiguousBases.Rd man/read.nexus.data.Rd man/CADM.global.Rd man/as.matching.Rd man/nodelabels.Rd man/corBlomberg.Rd man/write.nexus.data.Rd man/Initialize.corPhyl.Rd man/rTraitDisc.Rd man/corClasses.Rd man/cherry.Rd man/plot.correlogram.Rd man/carnivora.Rd man/apetools.Rd man/image.DNAbin.Rd man/diversi.gof.Rd man/as.bitsplits.Rd man/ape-internal.Rd man/mixedFontLabel.Rd man/makeNodeLabel.Rd man/coalescent.intervals.Rd man/edges.Rd man/rTraitCont.Rd man/richness.yule.test.Rd man/varcomp.Rd man/njs.Rd man/latag2n.Rd man/checkAlignment.Rd man/AAbin.Rd man/def.Rd man/clustal.Rd man/balance.Rd man/which.edge.Rd man/ace.Rd man/phydataplot.Rd man/yule.cov.Rd man/node.dating.Rd man/mat5M3ID.Rd man/chiroptera.Rd man/compar.ou.Rd man/ewLasso.Rd man/del.gaps.Rd man/chronos.Rd man/rTraitMult.Rd man/trex.Rd man/LTT.Rd man/reconstruct.Rd man/varCompPhylip.Rd man/read.tree.Rd man/is.binary.tree.Rd man/bird.families.Rd man/chronopl.Rd man/comparePhylo.Rd man/plot.varcomp.Rd man/degree.Rd man/unique.multiPhylo.Rd man/fastme.Rd man/subtrees.Rd man/bird.orders.Rd man/identify.phylo.Rd man/correlogram.formula.Rd man/where.Rd man/mat5Mrand.Rd man/delta.plot.Rd man/pcoa.Rd man/getAnnotationsGenBank.Rd man/diversi.time.Rd man/consensus.Rd man/read.dna.Rd man/vcv.phylo.Rd man/read.GenBank.Rd man/rDNAbin.Rd man/vcv2phylo.Rd man/pic.Rd man/as.alignment.Rd man/howmanytrees.Rd man/read.nexus.Rd man/all.equal.phylo.Rd man/yule.Rd man/diversity.contrast.test.Rd man/write.nexus.Rd man/MoranI.Rd man/is.monophyletic.Rd man/bind.tree.Rd man/MPR.Rd man/compar.gee.Rd man/yule.time.Rd man/corPagel.Rd man/treePop.Rd man/is.compatible.Rd man/corMartins.Rd man/kronoviz.Rd man/as.phylo.formula.Rd man/mcconwaysims.test.Rd man/cynipids.Rd man/plot.phyloExtra.Rd man/mat3.Rd man/gammaStat.Rd man/ladderize.Rd man/mvr.Rd man/as.phylo.Rd man/compute.brtime.Rd man/phymltest.Rd man/write.tree.Rd man/updateLabel.Rd man/rtt.Rd man/multiphylo.Rd man/compar.lynch.Rd man/alex.Rd man/plot.phylo.Rd man/parafit.Rd man/mst.Rd man/slowinskiguyer.test.Rd man/dist.gene.Rd man/seg.sites.Rd man/pic.ortho.Rd man/bd.ext.Rd