dataGeneTreeSample | Simulated gene tree dataset from species tree |
dataHeliconiusMartin | Heliconius gene tree dataset |
dataYeastRokas | Yeast gene tree dataset |
estimateEdgeLengths | Estimate edge lengths on a species tree from gene tree... |
expectedCFs | Produce table of expected quartet concordance factors for a... |
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 |
nexusDist | Write a distance table to a file in nexus format |
powerDivStat | Power divergence statistic of Cressie & Read |
pvalHist | Plot histogram of log p-values in table |
QDC | Compute Quartet Distance Consensus tree from gene tree data |
QDS | Compute Quartet Distance Supertree |
quartetDist | Compute quartet distance between taxa |
quartetNetworkDist | Compute network quartet distance between taxa |
quartetStarTest | Hypothesis test for quartet counts fitting a star tree under... |
quartetStarTestInd | Multiple independent hypothesis tests for gene quartet counts... |
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... |
quartetTableParallel | Produce table of counts of quartets displayed on trees, in... |
quartetTablePrint | Print a quartet table with nice formatting |
quartetTableResolved | Modify quartet table to show only resolved quartets |
quartetTestPlot | Produce simplex plot with results of quartet hypothesis tests |
quartetTreeErrorProb | Bayesian posterior probability of error in 4-taxon unrooted... |
quartetTreeTest | Hypothesis test for quartet counts fitting a tree under the... |
quartetTreeTestInd | Multiple independent hypothesis tests for quartet counts... |
quartetWeightedDist | Compute the Weighted Quartet Distance between taxa |
simplexCoords | Convert 3-d coordinates to 2-d probability simplex... |
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... |
simplexSegment | Plot line segment in 2-d probability simplex |
simplexText | Add text at a point in 2-d probability simplex |
T1density | Probability density function for Model T1 of... |
T3density | Probability density function for Model T3 of... |
taxonNames | Get all taxon names from a collection of trees |
WQDC | Compute Weighted Quartet Distance Consensus tree from gene... |
WQDCrecursive | Compute the Recursive Weighted Quartet Distance Consensus... |
WQDS | Compute the Weighted Quartet Distance Supertree |
WQDSAdjustLengths | Adjust edge lengths on tree built from Weighted Quartet... |
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