Files in gjuggler/ape
Analyses of Phylogenetics and Evolution
COPYING
ChangeLog
DESCRIPTION
NAMESPACE
R/CDAM.global.R
R/CDAM.post.R
R/CDF.birth.death.R
R/Cheverud.R
R/DNA.R
R/MPR.R
R/MoranI.R
R/PGLS.R
R/ace.R
R/all.equal.phylo.R
R/ape-defunct.R
R/as.matching.R
R/as.phylo.R
R/as.phylo.formula.R
R/balance.R
R/bind.tree.R
R/biplot.pcoa.R
R/birthdeath.R
R/branching.times.R
R/cherry.R
R/chronoMPL.R
R/chronopl.R
R/coalescent.intervals.R
R/collapse.singles.R
R/collapsed.intervals.R
R/compar.gee.R
R/compar.lynch.R
R/compar.ou.R
R/cophenetic.phylo.R
R/cophyloplot.R
R/delta.plot.R
R/dist.gene.R
R/dist.topo.R
R/diversi.gof.R
R/diversi.time.R
R/drop.tip.R
R/extract.popsize.R
R/gammaStat.R
R/howmanytrees.R
R/identify.phylo.R
R/is.binary.tree.R
R/is.monophyletic.R
R/is.ultrametric.R
R/ladderize.R
R/lmorigin.R
R/ltt.plot.R
R/makeLabel.R
R/makeNodeLabel.R
R/mantel.test.R
R/matexpo.R
R/mcmc.popsize.R
R/me.R
R/mrca.R
R/mst.R
R/multi2di.R
R/nj.R
R/nodelabels.R
R/parafit.R
R/pcoa.R
R/phymltest.R
R/pic.R
R/plot.phylo.R
R/plot.popsize.R
R/plotPhyloCoor.R
R/print.lmorigin.R
R/print.parafit.R
R/rTrait.R
R/read.GenBank.R
R/read.caic.R
R/read.dna.R
R/read.nexus.R
R/read.nexus.data.R
R/read.nhx.R
R/read.tree.R
R/reorder.phylo.R
R/root.R
R/rotate.R
R/rtree.R
R/scales.R
R/skyline.R
R/skylineplot.R
R/speciesTree.R
R/subtreeplot.R
R/subtrees.R
R/summary.phylo.R
R/unique.multiPhylo.R
R/varcomp.R
R/vcv.phylo.R
R/which.edge.R
R/write.dna.R
R/write.nexus.R
R/write.nexus.data.R
R/write.tree.R
R/yule.R
R/yule.time.R
R/zoom.R
R/zzz.R
Thanks
data/HP.links.rda
data/bird.families.R
data/bird.families.tre
data/bird.orders.R
data/bird.orders.tre
data/carnivora.csv
data/chiroptera.rda
data/cynipids.R
data/cynipids.txt
data/gopher.D.rda
data/hivtree.newick.R
data/hivtree.table.txt
data/landplants.newick.R
data/lice.D.rda
data/lmorigin.ex1.rda
data/lmorigin.ex2.rda
data/mat3.RData
data/mat5M3ID.RData
data/mat5Mrand.RData
data/opsin.newick.R
data/woodmouse.R
data/woodmouse.txt
inst/CITATION
inst/doc/MoranI.Rnw
inst/doc/MoranI.pdf
inst/doc/ape.bib
man/CADM.global.Rd
man/DNAbin.Rd
man/GC.content.Rd
man/Initialize.corPhyl.Rd
man/MPR.Rd
man/MoranI.Rd
man/ace.Rd
man/add.scale.bar.Rd
man/all.equal.phylo.Rd
man/ape-defunct.Rd
man/ape-internal.Rd
man/ape-package.Rd
man/as.alignment.Rd
man/as.matching.Rd
man/as.phylo.Rd
man/as.phylo.formula.Rd
man/axisPhylo.Rd
man/balance.Rd
man/base.freq.Rd
man/bd.ext.Rd
man/bd.time.Rd
man/bind.tree.Rd
man/bionj.Rd
man/bird.families.Rd
man/bird.orders.Rd
man/birthdeath.Rd
man/boot.phylo.Rd
man/branching.times.Rd
man/c.phylo.Rd
man/carnivora.Rd
man/cherry.Rd
man/chiroptera.Rd
man/chronoMPL.Rd
man/chronopl.Rd
man/coalescent.intervals.Rd
man/collapse.singles.Rd
man/collapsed.intervals.Rd
man/compar.cheverud.Rd
man/compar.gee.Rd
man/compar.lynch.Rd
man/compar.ou.Rd
man/compute.brlen.Rd
man/consensus.Rd
man/cophenetic.phylo.Rd
man/cophyloplot.Rd
man/corBlomberg.Rd
man/corBrownian.Rd
man/corClasses.Rd
man/corGrafen.Rd
man/corMartins.Rd
man/corPagel.Rd
man/correlogram.formula.Rd
man/cynipids.Rd
man/del.gaps.Rd
man/delta.plot.Rd
man/dist.dna.Rd
man/dist.gene.Rd
man/dist.topo.Rd
man/diversi.gof.Rd
man/diversi.time.Rd
man/drop.tip.Rd
man/edges.Rd
man/fastme.Rd
man/gammaStat.Rd
man/hivtree.Rd
man/howmanytrees.Rd
man/identify.phylo.Rd
man/is.binary.tree.Rd
man/is.monophyletic.Rd
man/is.ultrametric.Rd
man/ladderize.Rd
man/landplants.Rd
man/lmorigin.Rd
man/ltt.plot.Rd
man/makeLabel.Rd
man/makeNodeLabel.Rd
man/mantel.test.Rd
man/mat3.Rd
man/mat5M3ID.Rd
man/mat5Mrand.Rd
man/matexpo.Rd
man/mcmc.popsize.Rd
man/mixedFontLabel.Rd
man/mrca.Rd
man/mst.Rd
man/multi2di.Rd
man/multiphylo.Rd
man/nj.Rd
man/node.depth.Rd
man/nodelabels.Rd
man/opsin.Rd
man/parafit.Rd
man/pcoa.Rd
man/phymltest.Rd
man/pic.Rd
man/pic.ortho.Rd
man/plot.correlogram.Rd
man/plot.phylo.Rd
man/plot.varcomp.Rd
man/print.phylo.Rd
man/rTraitCont.Rd
man/rTraitDisc.Rd
man/read.GenBank.Rd
man/read.caic.Rd
man/read.dna.Rd
man/read.nexus.Rd
man/read.nexus.data.Rd
man/read.tree.Rd
man/reorder.phylo.Rd
man/rlineage.Rd
man/root.Rd
man/rotate.Rd
man/rtree.Rd
man/seg.sites.Rd
man/skyline.Rd
man/skylineplot.Rd
man/speciesTree.Rd
man/stree.Rd
man/subtreeplot.Rd
man/subtrees.Rd
man/summary.phylo.Rd
man/unique.multiPhylo.Rd
man/varCompPhylip.Rd
man/varcomp.Rd
man/vcv.phylo.Rd
man/weight.taxo.Rd
man/which.edge.Rd
man/woodmouse.Rd
man/write.dna.Rd
man/write.nexus.Rd
man/write.nexus.data.Rd
man/write.tree.Rd
man/yule.Rd
man/yule.cov.Rd
man/yule.time.Rd
man/zoom.Rd
src/BIONJ.c
src/BIONJ.o
src/Makevars
src/NNI.c
src/NNI.o
src/SPR.c
src/SPR.o
src/TBR.c
src/TBR.o
src/ape.so
src/bNNI.c
src/bNNI.o
src/bipartition.c
src/bipartition.o
src/delta_plot.c
src/delta_plot.o
src/dist_dna.c
src/dist_dna.o
src/heap.c
src/heap.o
src/mat_expo.c
src/mat_expo.o
src/me.c
src/me.h
src/me.o
src/me_balanced.c
src/me_balanced.o
src/me_ols.c
src/me_ols.o
src/newick.c
src/newick.o
src/nj.c
src/nj.o
src/pic.c
src/pic.o
src/plot_phylo.c
src/plot_phylo.o
src/rTrait.c
src/rTrait.o
src/reorder_phylo.c
src/reorder_phylo.o
src/tree_build.c
src/tree_build.o
src/tree_phylo.c
src/tree_phylo.o
test/tree_io.R
