# Analyzing Gene Tree Quartets under the Multi-Species Coalescent

## Documentation for package ‘MSCquartets’ version 3.2

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## Help Pages

MSCquartets-package | Multispecies Coalescent Model Quartet Package
allPerms | Generate permutations
blobDistance | Compute empirical distance between taxon groups.
BQinference | Main loop of B-quartet inference
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
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
expectedCFs | Produce table of expected quartet concordance factors for a species tree
expmodNANUQCycleDist | Expected modNANUQ cycle distance
expNANUQCycleDist | Expected NANUQ cycle distance
fitCycleOrders | Compute fit of circular orders to distance with least squares
HolmBonferroni | Apply Holm-Bonferroni method to adjust for multiple tests
initBquartets | Initialize vector of B quartets
labelIntNodes | Label internal nodes on tree
M0 | Modified Struve function
MSCquartets | 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
nodeGroups | Groups taxa by deleting a node in a tree
ordersHeuristicmodNANUQ | Choose cycle orders heuristically from empirical modNANUQ distance
powerDivStat | Power divergence statistic of Cressie & Read
pTableYeastRokas | pTable for Yeast dataset
pvalHist | Plot histogram of log p-values in table
QDC | Compute Quartet Distance Consensus tree from gene tree data
QDS | Compute Quartet Distance Supertree
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
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
T1density | Probability density function for Model T1
T3density | Probability density function for Model T3
tableHeleconiusMartin | Quartet table for Heliconius gene tree dataset
tableHeliconiusMartin | Quartet table for Heliconius gene tree dataset
tableLeopardusLescroart | Quartet table for Leopardus dataset
taxonNames | Get all taxon names from a collection of trees
TINNIK | TINNIK algorithm to infer species tree of blobs
TINNIKdist | Compute TINNIK distance from quartets and hypothesis test p-values
topDist | Topological distances on a tree
treeFromSplits | Produce tree from compatible splits
treeOfBlobs | Tree of blobs for a network
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