Man pages for MSCquartets
Analyzing Gene Tree Quartets under the Multi-Species Coalescent

dataGeneTreeSampleSimulated gene tree dataset from species tree
dataHeliconiusMartinHeliconius gene tree dataset
dataYeastRokasYeast gene tree dataset
estimateEdgeLengthsEstimate edge lengths on a species tree from gene tree...
expectedCFsProduce table of expected quartet concordance factors for a...
HolmBonferroniApply Holm-Bonferroni method to adjust for multiple tests
MSCquartets-packageMultispecies Coalescent Model Quartet Package
NANUQApply NANUQ network inference algorithm to gene tree data
NANUQdistCompute NANUQ distance and write to file
nexusDistWrite a distance table to a file in nexus format
powerDivStatPower divergence statistic of Cressie & Read
pvalHistPlot histogram of log p-values in table
QDCCompute Quartet Distance Consensus tree from gene tree data
QDSCompute Quartet Distance Supertree
quartetDistCompute quartet distance between taxa
quartetNetworkDistCompute network quartet distance between taxa
quartetStarTestHypothesis test for quartet counts fitting a star tree under...
quartetStarTestIndMultiple independent hypothesis tests for gene quartet counts...
quartetTableProduce table of counts of quartets displayed on trees
quartetTableCollapseReduce quartet table by combining some taxa
quartetTableDominantProduce table of dominant quartets, with estimates of...
quartetTableParallelProduce table of counts of quartets displayed on trees, in...
quartetTablePrintPrint a quartet table with nice formatting
quartetTableResolvedModify quartet table to show only resolved quartets
quartetTestPlotProduce simplex plot with results of quartet hypothesis tests
quartetTreeErrorProbBayesian posterior probability of error in 4-taxon unrooted...
quartetTreeTestHypothesis test for quartet counts fitting a tree under the...
quartetTreeTestIndMultiple independent hypothesis tests for quartet counts...
quartetWeightedDistCompute the Weighted Quartet Distance between taxa
simplexCoordsConvert 3-d coordinates to 2-d probability simplex...
simplexLabelsLabel vertices of 2-d probability simplex
simplexPointPlot point in 2-d probability simplex
simplexPrepareDraw 2-d probability simplex, with model lines for T3 or T1...
simplexSegmentPlot line segment in 2-d probability simplex
simplexTextAdd text at a point in 2-d probability simplex
T1densityProbability density function for Model T1 of...
T3densityProbability density function for Model T3 of...
taxonNamesGet all taxon names from a collection of trees
WQDCCompute Weighted Quartet Distance Consensus tree from gene...
WQDCrecursiveCompute the Recursive Weighted Quartet Distance Consensus...
WQDSCompute the Weighted Quartet Distance Supertree
WQDSAdjustLengthsAdjust edge lengths on tree built from Weighted Quartet...
MSCquartets documentation built on April 19, 2022, 5:08 p.m.