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<head><title>R: Phylogenetic Reconstruction and Analysis</title>
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<h1> Phylogenetic Reconstruction and Analysis
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</div><h2>Documentation for package ‘phangorn’ version 2.4.0</h2>
<ul><li><a href="../DESCRIPTION">DESCRIPTION file</a>.</li>
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<h2>Help Pages</h2>
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<table width="100%">
<tr><td style="width: 25%;"><a href="phangorn-package.html">phangorn-package</a></td>
<td>Phylogenetic analysis in R</td></tr>
</table>
<h2><a name="A">-- A --</a></h2>
<table width="100%">
<tr><td style="width: 25%;"><a href="parsimony.html">acctran</a></td>
<td>Parsimony tree.</td></tr>
<tr><td style="width: 25%;"><a href="phyDat.html">acgt2ry</a></td>
<td>Conversion among Sequence Formats</td></tr>
<tr><td style="width: 25%;"><a href="add.tips.html">add.tips</a></td>
<td>Add tips to a tree</td></tr>
<tr><td style="width: 25%;"><a href="addConfidences.html">addConfidences</a></td>
<td>Compare splits and add support values to an object</td></tr>
<tr><td style="width: 25%;"><a href="as.splits.html">addTrivialSplits</a></td>
<td>Splits representation of graphs and trees.</td></tr>
<tr><td style="width: 25%;"><a href="modelTest.html">AICc</a></td>
<td>ModelTest</td></tr>
<tr><td style="width: 25%;"><a href="as.splits.html">allCircularSplits</a></td>
<td>Splits representation of graphs and trees.</td></tr>
<tr><td style="width: 25%;"><a href="phyDat.html">allSitePattern</a></td>
<td>Conversion among Sequence Formats</td></tr>
<tr><td style="width: 25%;"><a href="as.splits.html">allSplits</a></td>
<td>Splits representation of graphs and trees.</td></tr>
<tr><td style="width: 25%;"><a href="allTrees.html">allTrees</a></td>
<td>Compute all trees topologies.</td></tr>
<tr><td style="width: 25%;"><a href="ancestral.pml.html">ancestral.pars</a></td>
<td>Ancestral character reconstruction.</td></tr>
<tr><td style="width: 25%;"><a href="ancestral.pml.html">ancestral.pml</a></td>
<td>Ancestral character reconstruction.</td></tr>
<tr><td style="width: 25%;"><a href="phyDat.html">as.AAbin.phyDat</a></td>
<td>Conversion among Sequence Formats</td></tr>
<tr><td style="width: 25%;"><a href="as.splits.html">as.bitsplits.splits</a></td>
<td>Splits representation of graphs and trees.</td></tr>
<tr><td style="width: 25%;"><a href="phyDat.html">as.character.phyDat</a></td>
<td>Conversion among Sequence Formats</td></tr>
<tr><td style="width: 25%;"><a href="phyDat.html">as.data.frame.phyDat</a></td>
<td>Conversion among Sequence Formats</td></tr>
<tr><td style="width: 25%;"><a href="phyDat.html">as.DNAbin.phyDat</a></td>
<td>Conversion among Sequence Formats</td></tr>
<tr><td style="width: 25%;"><a href="as.splits.html">as.Matrix</a></td>
<td>Splits representation of graphs and trees.</td></tr>
<tr><td style="width: 25%;"><a href="as.splits.html">as.Matrix.splits</a></td>
<td>Splits representation of graphs and trees.</td></tr>
<tr><td style="width: 25%;"><a href="as.splits.html">as.matrix.splits</a></td>
<td>Splits representation of graphs and trees.</td></tr>
<tr><td style="width: 25%;"><a href="phyDat.html">as.MultipleAlignment</a></td>
<td>Conversion among Sequence Formats</td></tr>
<tr><td style="width: 25%;"><a href="phyDat.html">as.MultipleAlignment.phyDat</a></td>
<td>Conversion among Sequence Formats</td></tr>
<tr><td style="width: 25%;"><a href="as.networx.html">as.networx</a></td>
<td>Phylogenetic networks</td></tr>
<tr><td style="width: 25%;"><a href="as.networx.html">as.networx.phylo</a></td>
<td>Phylogenetic networks</td></tr>
<tr><td style="width: 25%;"><a href="as.networx.html">as.networx.splits</a></td>
<td>Phylogenetic networks</td></tr>
<tr><td style="width: 25%;"><a href="phyDat.html">as.phyDat</a></td>
<td>Conversion among Sequence Formats</td></tr>
<tr><td style="width: 25%;"><a href="phyDat.html">as.phyDat.alignment</a></td>
<td>Conversion among Sequence Formats</td></tr>
<tr><td style="width: 25%;"><a href="phyDat.html">as.phyDat.character</a></td>
<td>Conversion among Sequence Formats</td></tr>
<tr><td style="width: 25%;"><a href="phyDat.html">as.phyDat.data.frame</a></td>
<td>Conversion among Sequence Formats</td></tr>
<tr><td style="width: 25%;"><a href="phyDat.html">as.phyDat.DNAbin</a></td>
<td>Conversion among Sequence Formats</td></tr>
<tr><td style="width: 25%;"><a href="phyDat.html">as.phyDat.factor</a></td>
<td>Conversion among Sequence Formats</td></tr>
<tr><td style="width: 25%;"><a href="phyDat.html">as.phyDat.matrix</a></td>
<td>Conversion among Sequence Formats</td></tr>
<tr><td style="width: 25%;"><a href="phyDat.html">as.phyDat.MultipleAlignment</a></td>
<td>Conversion among Sequence Formats</td></tr>
<tr><td style="width: 25%;"><a href="as.splits.html">as.phylo.splits</a></td>
<td>Splits representation of graphs and trees.</td></tr>
<tr><td style="width: 25%;"><a href="as.splits.html">as.prop.part.splits</a></td>
<td>Splits representation of graphs and trees.</td></tr>
<tr><td style="width: 25%;"><a href="as.splits.html">as.splits</a></td>
<td>Splits representation of graphs and trees.</td></tr>
<tr><td style="width: 25%;"><a href="as.splits.html">as.splits.multiPhylo</a></td>
<td>Splits representation of graphs and trees.</td></tr>
<tr><td style="width: 25%;"><a href="as.splits.html">as.splits.networx</a></td>
<td>Splits representation of graphs and trees.</td></tr>
<tr><td style="width: 25%;"><a href="as.splits.html">as.splits.phylo</a></td>
<td>Splits representation of graphs and trees.</td></tr>
</table>
<h2><a name="B">-- B --</a></h2>
<table width="100%">
<tr><td style="width: 25%;"><a href="bab.html">bab</a></td>
<td>Branch and bound for finding all most parsimonious trees</td></tr>
<tr><td style="width: 25%;"><a href="phyDat.html">baseFreq</a></td>
<td>Conversion among Sequence Formats</td></tr>
<tr><td style="width: 25%;"><a href="bootstrap.pml.html">bootstrap.phyDat</a></td>
<td>Bootstrap</td></tr>
<tr><td style="width: 25%;"><a href="bootstrap.pml.html">bootstrap.pml</a></td>
<td>Bootstrap</td></tr>
<tr><td style="width: 25%;"><a href="bab.html">BranchAndBound</a></td>
<td>Branch and bound for finding all most parsimonious trees</td></tr>
</table>
<h2><a name="C">-- C --</a></h2>
<table width="100%">
<tr><td style="width: 25%;"><a href="phyDat.html">c.phyDat</a></td>
<td>Conversion among Sequence Formats</td></tr>
<tr><td style="width: 25%;"><a href="as.splits.html">c.splits</a></td>
<td>Splits representation of graphs and trees.</td></tr>
<tr><td style="width: 25%;"><a href="phyDat.html">cbind.phyDat</a></td>
<td>Conversion among Sequence Formats</td></tr>
<tr><td style="width: 25%;"><a href="chloroplast.html">chloroplast</a></td>
<td>Chloroplast alignment</td></tr>
<tr><td style="width: 25%;"><a href="CI.html">CI</a></td>
<td>Consistency Index and Retention Index</td></tr>
<tr><td style="width: 25%;"><a href="cladePar.html">cladePar</a></td>
<td>Utility function to plot.phylo</td></tr>
<tr><td style="width: 25%;"><a href="coalSpeciesTree.html">coalSpeciesTree</a></td>
<td>Species Tree</td></tr>
<tr><td style="width: 25%;"><a href="phyDat.html">codon2dna</a></td>
<td>Conversion among Sequence Formats</td></tr>
<tr><td style="width: 25%;"><a href="as.splits.html">compatible</a></td>
<td>Splits representation of graphs and trees.</td></tr>
<tr><td style="width: 25%;"><a href="consensusNet.html">consensusNet</a></td>
<td>Computes a consensusNetwork from a list of trees Computes a 'networx' object from a collection of splits.</td></tr>
<tr><td style="width: 25%;"><a href="cophenetic.networx.html">cophenetic.networx</a></td>
<td>Pairwise Distances from a Phylogenetic Network</td></tr>
<tr><td style="width: 25%;"><a href="cophenetic.networx.html">cophenetic.splits</a></td>
<td>Pairwise Distances from a Phylogenetic Network</td></tr>
<tr><td style="width: 25%;"><a href="addConfidences.html">createLabel</a></td>
<td>Compare splits and add support values to an object</td></tr>
</table>
<h2><a name="D">-- D --</a></h2>
<table width="100%">
<tr><td style="width: 25%;"><a href="delta.score.html">delta.score</a></td>
<td>Computes the delta score</td></tr>
<tr><td style="width: 25%;"><a href="densiTree.html">densiTree</a></td>
<td>Plots a densiTree.</td></tr>
<tr><td style="width: 25%;"><a href="designTree.html">designSplits</a></td>
<td>Compute a design matrix or non-negative LS</td></tr>
<tr><td style="width: 25%;"><a href="designTree.html">designTree</a></td>
<td>Compute a design matrix or non-negative LS</td></tr>
<tr><td style="width: 25%;"><a href="dfactorial.html">dfactorial</a></td>
<td>Arithmetic Operators</td></tr>
<tr><td style="width: 25%;"><a href="pml.fit.html">discrete.gamma</a></td>
<td>Internal maximum likelihood functions.</td></tr>
<tr><td style="width: 25%;"><a href="dist.hamming.html">dist.hamming</a></td>
<td>Pairwise Distances from Sequences</td></tr>
<tr><td style="width: 25%;"><a href="dist.hamming.html">dist.logDet</a></td>
<td>Pairwise Distances from Sequences</td></tr>
<tr><td style="width: 25%;"><a href="dist.hamming.html">dist.ml</a></td>
<td>Pairwise Distances from Sequences</td></tr>
<tr><td style="width: 25%;"><a href="dist.p.html">dist.p</a></td>
<td>Pairwise Polymorphism P-Distances from DNA Sequences</td></tr>
<tr><td style="width: 25%;"><a href="distanceHadamard.html">distanceHadamard</a></td>
<td>Distance Hadamard</td></tr>
<tr><td style="width: 25%;"><a href="as.splits.html">distinct.splits</a></td>
<td>Splits representation of graphs and trees.</td></tr>
<tr><td style="width: 25%;"><a href="getClans.html">diversity</a></td>
<td>Clans, slices and clips</td></tr>
<tr><td style="width: 25%;"><a href="phyDat.html">dna2codon</a></td>
<td>Conversion among Sequence Formats</td></tr>
</table>
<h2><a name="E">-- E --</a></h2>
<table width="100%">
<tr><td style="width: 25%;"><a href="pml.fit.html">edQt</a></td>
<td>Internal maximum likelihood functions.</td></tr>
</table>
<h2><a name="F">-- F --</a></h2>
<table width="100%">
<tr><td style="width: 25%;"><a href="hadamard.html">fhm</a></td>
<td>Hadamard Matrices and Fast Hadamard Multiplication</td></tr>
<tr><td style="width: 25%;"><a href="parsimony.html">fitch</a></td>
<td>Parsimony tree.</td></tr>
</table>
<h2><a name="G">-- G --</a></h2>
<table width="100%">
<tr><td style="width: 25%;"><a href="phyDat.html">genlight2phyDat</a></td>
<td>Conversion among Sequence Formats</td></tr>
<tr><td style="width: 25%;"><a href="getClans.html">getClans</a></td>
<td>Clans, slices and clips</td></tr>
<tr><td style="width: 25%;"><a href="getClans.html">getClips</a></td>
<td>Clans, slices and clips</td></tr>
<tr><td style="width: 25%;"><a href="getClans.html">getDiversity</a></td>
<td>Clans, slices and clips</td></tr>
<tr><td style="width: 25%;"><a href="midpoint.html">getRoot</a></td>
<td>Tree manipulation</td></tr>
<tr><td style="width: 25%;"><a href="getClans.html">getSlices</a></td>
<td>Clans, slices and clips</td></tr>
</table>
<h2><a name="H">-- H --</a></h2>
<table width="100%">
<tr><td style="width: 25%;"><a href="hadamard.html">h2st</a></td>
<td>Hadamard Matrices and Fast Hadamard Multiplication</td></tr>
<tr><td style="width: 25%;"><a href="hadamard.html">h4st</a></td>
<td>Hadamard Matrices and Fast Hadamard Multiplication</td></tr>
<tr><td style="width: 25%;"><a href="hadamard.html">hadamard</a></td>
<td>Hadamard Matrices and Fast Hadamard Multiplication</td></tr>
</table>
<h2><a name="I">-- I --</a></h2>
<table width="100%">
<tr><td style="width: 25%;"><a href="identify.networx.html">identify.networx</a></td>
<td>Identify splits in a network</td></tr>
<tr><td style="width: 25%;"><a href="phyDat.html">image.phyDat</a></td>
<td>Conversion among Sequence Formats</td></tr>
</table>
<h2><a name="K">-- K --</a></h2>
<table width="100%">
<tr><td style="width: 25%;"><a href="treedist.html">KF.dist</a></td>
<td>Distances between trees</td></tr>
</table>
<h2><a name="L">-- L --</a></h2>
<table width="100%">
<tr><td style="width: 25%;"><a href="Laurasiatherian.html">Laurasiatherian</a></td>
<td>Laurasiatherian data (AWCMEE)</td></tr>
<tr><td style="width: 25%;"><a href="dfactorial.html">ldfactorial</a></td>
<td>Arithmetic Operators</td></tr>
<tr><td style="width: 25%;"><a href="lento.html">lento</a></td>
<td>Lento plot</td></tr>
<tr><td style="width: 25%;"><a href="pml.fit.html">lli</a></td>
<td>Internal maximum likelihood functions.</td></tr>
</table>
<h2><a name="M">-- M --</a></h2>
<table width="100%">
<tr><td style="width: 25%;"><a href="mast.html">mast</a></td>
<td>Maximum agreement subtree</td></tr>
<tr><td style="width: 25%;"><a href="as.splits.html">matchSplits</a></td>
<td>Splits representation of graphs and trees.</td></tr>
<tr><td style="width: 25%;"><a href="maxCladeCred.html">maxCladeCred</a></td>
<td>Maximum clade credibility tree</td></tr>
<tr><td style="width: 25%;"><a href="midpoint.html">midpoint</a></td>
<td>Tree manipulation</td></tr>
<tr><td style="width: 25%;"><a href="midpoint.html">midpoint.multiPhylo</a></td>
<td>Tree manipulation</td></tr>
<tr><td style="width: 25%;"><a href="midpoint.html">midpoint.phylo</a></td>
<td>Tree manipulation</td></tr>
<tr><td style="width: 25%;"><a href="modelTest.html">modelTest</a></td>
<td>ModelTest</td></tr>
<tr><td style="width: 25%;"><a href="pmlPart.html">multiphyDat2pmlPart</a></td>
<td>Partition model.</td></tr>
</table>
<h2><a name="N">-- N --</a></h2>
<table width="100%">
<tr><td style="width: 25%;"><a href="neighborNet.html">neighborNet</a></td>
<td>Computes a neighborNet from a distance matrix</td></tr>
<tr><td style="width: 25%;"><a href="as.networx.html">networx</a></td>
<td>Phylogenetic networks</td></tr>
<tr><td style="width: 25%;"><a href="NJ.html">NJ</a></td>
<td>Neighbor-Joining</td></tr>
<tr><td style="width: 25%;"><a href="nni.html">nni</a></td>
<td>Tree rearrangements.</td></tr>
<tr><td style="width: 25%;"><a href="designTree.html">nnls.networx</a></td>
<td>Compute a design matrix or non-negative LS</td></tr>
<tr><td style="width: 25%;"><a href="designTree.html">nnls.phylo</a></td>
<td>Compute a design matrix or non-negative LS</td></tr>
<tr><td style="width: 25%;"><a href="designTree.html">nnls.splits</a></td>
<td>Compute a design matrix or non-negative LS</td></tr>
<tr><td style="width: 25%;"><a href="designTree.html">nnls.tree</a></td>
<td>Compute a design matrix or non-negative LS</td></tr>
</table>
<h2><a name="O">-- O --</a></h2>
<table width="100%">
<tr><td style="width: 25%;"><a href="parsimony.html">optim.parsimony</a></td>
<td>Parsimony tree.</td></tr>
<tr><td style="width: 25%;"><a href="pml.html">optim.pml</a></td>
<td>Likelihood of a tree.</td></tr>
</table>
<h2><a name="P">-- P --</a></h2>
<table width="100%">
<tr><td style="width: 25%;"><a href="ancestral.pml.html">pace</a></td>
<td>Ancestral character reconstruction.</td></tr>
<tr><td style="width: 25%;"><a href="parsimony.html">parsimony</a></td>
<td>Parsimony tree.</td></tr>
<tr><td style="width: 25%;"><a href="treedist.html">path.dist</a></td>
<td>Distances between trees</td></tr>
<tr><td style="width: 25%;"><a href="phangorn-package.html">phangorn</a></td>
<td>Phylogenetic analysis in R</td></tr>
<tr><td style="width: 25%;"><a href="phyDat.html">phyDat</a></td>
<td>Conversion among Sequence Formats</td></tr>
<tr><td style="width: 25%;"><a href="phyDat.html">phyDat2alignment</a></td>
<td>Conversion among Sequence Formats</td></tr>
<tr><td style="width: 25%;"><a href="phyDat.html">phyDat2MultipleAlignment</a></td>
<td>Conversion among Sequence Formats</td></tr>
<tr><td style="width: 25%;"><a href="as.networx.html">plot.networx</a></td>
<td>Phylogenetic networks</td></tr>
<tr><td style="width: 25%;"><a href="ancestral.pml.html">plotAnc</a></td>
<td>Ancestral character reconstruction.</td></tr>
<tr><td style="width: 25%;"><a href="bootstrap.pml.html">plotBS</a></td>
<td>Bootstrap</td></tr>
<tr><td style="width: 25%;"><a href="pml.html">pml</a></td>
<td>Likelihood of a tree.</td></tr>
<tr><td style="width: 25%;"><a href="pml.html">pml.control</a></td>
<td>Likelihood of a tree.</td></tr>
<tr><td style="width: 25%;"><a href="pml.fit.html">pml.fit</a></td>
<td>Internal maximum likelihood functions.</td></tr>
<tr><td style="width: 25%;"><a href="pml.fit.html">pml.free</a></td>
<td>Internal maximum likelihood functions.</td></tr>
<tr><td style="width: 25%;"><a href="pml.fit.html">pml.init</a></td>
<td>Internal maximum likelihood functions.</td></tr>
<tr><td style="width: 25%;"><a href="pmlCluster.html">pmlCluster</a></td>
<td>Stochastic Partitioning</td></tr>
<tr><td style="width: 25%;"><a href="pmlMix.html">pmlMix</a></td>
<td>Phylogenetic mixture model</td></tr>
<tr><td style="width: 25%;"><a href="pmlPart.html">pmlPart</a></td>
<td>Partition model.</td></tr>
<tr><td style="width: 25%;"><a href="pmlPart.html">pmlPart2multiPhylo</a></td>
<td>Partition model.</td></tr>
<tr><td style="width: 25%;"><a href="pmlMix.html">pmlPen</a></td>
<td>Phylogenetic mixture model</td></tr>
<tr><td style="width: 25%;"><a href="NJ.html">PNJ</a></td>
<td>Neighbor-Joining</td></tr>
<tr><td style="width: 25%;"><a href="parsimony.html">pratchet</a></td>
<td>Parsimony tree.</td></tr>
<tr><td style="width: 25%;"><a href="addConfidences.html">presenceAbsence</a></td>
<td>Compare splits and add support values to an object</td></tr>
<tr><td style="width: 25%;"><a href="as.splits.html">print.splits</a></td>
<td>Splits representation of graphs and trees.</td></tr>
<tr><td style="width: 25%;"><a href="midpoint.html">pruneTree</a></td>
<td>Tree manipulation</td></tr>
</table>
<h2><a name="R">-- R --</a></h2>
<table width="100%">
<tr><td style="width: 25%;"><a href="parsimony.html">random.addition</a></td>
<td>Parsimony tree.</td></tr>
<tr><td style="width: 25%;"><a href="read.aa.html">read.aa</a></td>
<td>Read Amino Acid Sequences in a File</td></tr>
<tr><td style="width: 25%;"><a href="read.nexus.splits.html">read.nexus.networx</a></td>
<td>Function to import and export splits and networks</td></tr>
<tr><td style="width: 25%;"><a href="read.nexus.splits.html">read.nexus.splits</a></td>
<td>Function to import and export splits and networks</td></tr>
<tr><td style="width: 25%;"><a href="phyDat.html">read.phyDat</a></td>
<td>Conversion among Sequence Formats</td></tr>
<tr><td style="width: 25%;"><a href="writeDist.html">readDist</a></td>
<td>Writing and reading distances in phylip and nexus format</td></tr>
<tr><td style="width: 25%;"><a href="as.splits.html">removeTrivialSplits</a></td>
<td>Splits representation of graphs and trees.</td></tr>
<tr><td style="width: 25%;"><a href="phyDat.html">removeUndeterminedSites</a></td>
<td>Conversion among Sequence Formats</td></tr>
<tr><td style="width: 25%;"><a href="treedist.html">RF.dist</a></td>
<td>Distances between trees</td></tr>
<tr><td style="width: 25%;"><a href="CI.html">RI</a></td>
<td>Consistency Index and Retention Index</td></tr>
<tr><td style="width: 25%;"><a href="nni.html">rNNI</a></td>
<td>Tree rearrangements.</td></tr>
<tr><td style="width: 25%;"><a href="nni.html">rSPR</a></td>
<td>Tree rearrangements.</td></tr>
</table>
<h2><a name="S">-- S --</a></h2>
<table width="100%">
<tr><td style="width: 25%;"><a href="parsimony.html">sankoff</a></td>
<td>Parsimony tree.</td></tr>
<tr><td style="width: 25%;"><a href="SH.test.html">SH.test</a></td>
<td>Shimodaira-Hasegawa Test</td></tr>
<tr><td style="width: 25%;"><a href="simSeq.html">simSeq</a></td>
<td>Simulate sequences.</td></tr>
<tr><td style="width: 25%;"><a href="simSeq.html">simSeq.phylo</a></td>
<td>Simulate sequences.</td></tr>
<tr><td style="width: 25%;"><a href="simSeq.html">simSeq.pml</a></td>
<td>Simulate sequences.</td></tr>
<tr><td style="width: 25%;"><a href="SOWH.test.html">SOWH.test</a></td>
<td>Swofford-Olsen-Waddell-Hillis Test</td></tr>
<tr><td style="width: 25%;"><a href="as.splits.html">splits</a></td>
<td>Splits representation of graphs and trees.</td></tr>
<tr><td style="width: 25%;"><a href="splitsNetwork.html">splitsNetwork</a></td>
<td>Phylogenetic Network</td></tr>
<tr><td style="width: 25%;"><a href="treedist.html">SPR.dist</a></td>
<td>Distances between trees</td></tr>
<tr><td style="width: 25%;"><a href="treedist.html">sprdist</a></td>
<td>Distances between trees</td></tr>
<tr><td style="width: 25%;"><a href="phyDat.html">subset.phyDat</a></td>
<td>Conversion among Sequence Formats</td></tr>
<tr><td style="width: 25%;"><a href="superTree.html">superTree</a></td>
<td>Super Tree methods</td></tr>
</table>
<h2><a name="T">-- T --</a></h2>
<table width="100%">
<tr><td style="width: 25%;"><a href="treedist.html">treedist</a></td>
<td>Distances between trees</td></tr>
</table>
<h2><a name="U">-- U --</a></h2>
<table width="100%">
<tr><td style="width: 25%;"><a href="writeDist.html">unique.dist</a></td>
<td>Writing and reading distances in phylip and nexus format</td></tr>
<tr><td style="width: 25%;"><a href="phyDat.html">unique.phyDat</a></td>
<td>Conversion among Sequence Formats</td></tr>
<tr><td style="width: 25%;"><a href="as.splits.html">unique.splits</a></td>
<td>Splits representation of graphs and trees.</td></tr>
<tr><td style="width: 25%;"><a href="NJ.html">UNJ</a></td>
<td>Neighbor-Joining</td></tr>
<tr><td style="width: 25%;"><a href="upgma.html">upgma</a></td>
<td>UPGMA and WPGMA</td></tr>
</table>
<h2><a name="W">-- W --</a></h2>
<table width="100%">
<tr><td style="width: 25%;"><a href="upgma.html">wpgma</a></td>
<td>UPGMA and WPGMA</td></tr>
<tr><td style="width: 25%;"><a href="treedist.html">wRF.dist</a></td>
<td>Distances between trees</td></tr>
<tr><td style="width: 25%;"><a href="writeDist.html">write.nexus.dist</a></td>
<td>Writing and reading distances in phylip and nexus format</td></tr>
<tr><td style="width: 25%;"><a href="read.nexus.splits.html">write.nexus.networx</a></td>
<td>Function to import and export splits and networks</td></tr>
<tr><td style="width: 25%;"><a href="read.nexus.splits.html">write.nexus.splits</a></td>
<td>Function to import and export splits and networks</td></tr>
<tr><td style="width: 25%;"><a href="phyDat.html">write.phyDat</a></td>
<td>Conversion among Sequence Formats</td></tr>
<tr><td style="width: 25%;"><a href="read.nexus.splits.html">write.splits</a></td>
<td>Function to import and export splits and networks</td></tr>
<tr><td style="width: 25%;"><a href="writeDist.html">writeDist</a></td>
<td>Writing and reading distances in phylip and nexus format</td></tr>
</table>
<h2><a name="Y">-- Y --</a></h2>
<table width="100%">
<tr><td style="width: 25%;"><a href="yeast.html">yeast</a></td>
<td>Yeast alignment (Rokas et al.)</td></tr>
</table>
</body></html>
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