Analyzing Gene Tree Quartets under the Multi-Species Coalescent

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 |

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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