ASTRALtreeLeopardusLescroart
                        ASTRAL tree for Leopardus dataset
BQinference             Main loop of B-quartet inference
ECToBlob                Edge Contraction to infer a Tree of Blobs
ECToBlob_bi             Edge Contraction to infer a Tree of Blobs -
                        bipartition mode
ECToBlob_mul            Edge Contraction to infer a Tree of Blobs -
                        multipartition mode
ECToBlob_quad           Edge Contraction to infer a Tree of Blobs -
                        quadripartition mode
HolmBonferroni          Apply Holm-Bonferroni method to adjust for
                        multiple tests
M0                      Modified Struve function
MSCquartets-package     Multispecies Coalescent Model Quartet Package
NANUQ                   Apply NANUQ network inference algorithm to gene
                        tree data
NANUQdist               Compute NANUQ distance and write to file
QDC                     Compute Quartet Distance Consensus tree from
                        gene tree data
QDS                     Compute Quartet Distance Supertree
T1density               Probability density function for Model T1
T3density               Probability density function for Model T3
TINNIK                  TINNIK algorithm to infer species tree of blobs
TINNIKdist              Compute TINNIK distance from quartets and
                        hypothesis test p-values
WQDC                    Compute Weighted Quartet Distance Consensus
                        tree from gene tree data
WQDCrecursive           Compute the Recursive Weighted Quartet Distance
                        Consensus tree from gene tree data
WQDS                    Compute the Weighted Quartet Distance Supertree
WQDSAdjustLengths       Adjust edge lengths on tree built from Weighted
                        Quartet distance to estimate metric tree
allPerms                Generate permutations
blobDistance            Compute empirical distance between taxon
                        groups.
circHybOrders           Generate all circular orders with designated
                        hybrid
collapseEdges           Collapse short tree edges
combineCycleResolutions
                        Combine several cycle resolutions on a tree of
                        blobs to create a network
combineP                Combine p-values of tests
compatibleSplits        Extract compatible splits
cutDensity              Probability density function for Cut Model
dataGeneTreeSample      Simulated gene tree dataset from species tree
dataPapioniniVanderpool
                        Papionini gene tree dataset
dataYeastRokas          Yeast gene tree dataset
estimateEdgeLengths     Estimate edge lengths on a species tree from
                        gene tree quartet counts
expNANUQCycleDist       Expected NANUQ cycle distance
expectedCFs             Produce table of expected quartet concordance
                        factors for a species tree
expmodNANUQCycleDist    Expected modNANUQ cycle distance
fitCycleOrders          Compute fit of circular orders to distance with
                        least squares
initBquartets           Initialize vector of B quartets
labelIntNodes           Label internal nodes on tree
nexusDist               Write a distance table to a file in nexus
                        format
nodeGroups              Groups taxa by deleting a node in a tree
ordersHeuristicmodNANUQ
                        Choose cycle orders heuristically from
                        empirical modNANUQ distance
pTableYeastRokas        pTable for Yeast dataset
powerDivStat            Power divergence statistic of Cressie & Read
pvalHist                Plot histogram of log p-values in table
quartetBTinferencePlot
                        Produce simplex plot with results of
                        B/T-quartet inference
quartetCutMLE           Maximum likelihood estimate of quartet tree of
                        blobs topology and CF under Cut model
quartetCutTest          Hypothesis test for quartet counts fitting a
                        resolved quartet tree of blobs under NMSC
quartetCutTestInd       Multiple independent hypothesis tests for
                        quartet counts fitting the Cut model under the
                        NMSC
quartetDist             Compute quartet distance between taxa
quartetDistTree         Build a Species Tree from Gene Trees Using the
                        Quartet Distance
quartetECtestInd        Hypothesis testing of quartet counts for
                        ECToBlob
quartetNetworkDist      Compute network quartet distance between taxa
quartetStarTest         Hypothesis test for quartet counts fitting a
                        star tree under the MSC
quartetStarTestInd      Multiple independent hypothesis tests for gene
                        quartet counts fitting a species quartet star
                        tree under the MSC
quartetTable            Produce table of counts of quartets displayed
                        on trees
quartetTableCollapse    Reduce quartet table by combining some taxa
quartetTableDominant    Produce table of dominant quartets, with
                        estimates of internal edge lengths
quartetTableParallel    Produce table of counts of quartets displayed
                        on trees, in parallel for large data sets
quartetTablePrint       Print a quartet table with nice formatting
quartetTableResolved    Modify quartet table to show only resolved
                        quartets
quartetTallyCpp         Build quartet table from distances
quartetTestPlot         Produce simplex plot with results of quartet
                        hypothesis tests
quartetTreeErrorProb    Bayesian posterior probability of error in
                        4-taxon unrooted species tree topology estimate
quartetTreeTest         Hypothesis test for quartet counts fitting a
                        tree under the MSC
quartetTreeTestInd      Multiple independent hypothesis tests for
                        quartet counts fitting a species tree under the
                        MSC
quartetWeightedDist     Compute the Weighted Quartet Distance between
                        taxa
resolveCycle            Resolve a node on a tree of blobs as a cycle
resolveLevel1           Resolve Tree of Blobs to Level-1 network
simplexCoords           Convert 3-d coordinates to 2-d probability
                        simplex coordinates
simplexLabels           Label vertices of 2-d probability simplex
simplexPoint            Plot point in 2-d probability simplex
simplexPrepare          Draw 2-d probability simplex, with model lines
                        for T3 or T1 model
simplexSegment          Plot line segment in 2-d probability simplex
simplexText             Add text at a point in 2-d probability simplex
sortQuartetTableRows    Sort quartet table rows by lex order
suppressNetBinaryNodes
                        Suppress Network Binary Nodes
tableHeliconiusMartin   Quartet table for Heliconius gene tree dataset
tableLeopardusLescroart
                        Quartet table for Leopardus dataset
taxonNames              Get all taxon names from a collection of trees
topDist                 Topological distances on a tree
treeFromSplits          Produce tree from compatible splits
treeOfBlobs             Tree of blobs for a network
