MSCquartets

Apply Holm-Bonferroni method to adjust for multiple tests

Multispecies Coalescent Model Quartet Package

Apply NANUQ network inference algorithm to gene tree data

Compute NANUQ distance and write to file

Compute Quartet Distance Consensus tree from gene tree data

Compute Quartet Distance Supertree

Probability density function for Model T1 of Mitchell et al. (2019), Proposition 5.2

Probability density function for Model T3 of Mitchell et al. (2019), Proposition 4.2

Compute Weighted Quartet Distance Consensus tree from gene tree data

Compute the Recursive Weighted Quartet Distance Consensus tree from gene tree data

Compute the Weighted Quartet Distance Supertree

Adjust edge lengths on tree built from Weighted Quartet distance to estimate metric tree

Simulated gene tree dataset from species tree

Heliconius gene tree dataset

Yeast gene tree dataset

Estimate edge lengths on a species tree from gene tree quartet counts

Produce table of expected quartet concordance factors for a species tree

Write a distance table to a file in nexus format

Power divergence statistic of Cressie & Read

Plot histogram of log p-values in table

Compute quartet distance between taxa

Compute network quartet distance between taxa

Hypothesis test for quartet counts fitting a star tree under the MSC

Multiple independent hypothesis tests for gene quartet counts fitting a species quartet star tree under the MSC

Produce table of counts of quartets displayed on trees

Reduce quartet table by combining some taxa

Produce table of dominant quartets, with estimates of internal edge lengths

Produce table of counts of quartets displayed on trees, in parallel for large data sets

Print a quartet table with nice formatting

Modify quartet table to show only resolved quartets

Produce simplex plot with results of quartet hypothesis tests

Bayesian posterior probability of error in 4-taxon unrooted species tree topology estimate

Hypothesis test for quartet counts fitting a tree under the MSC

Multiple independent hypothesis tests for quartet counts fitting a species tree under the MSC

Compute the Weighted Quartet Distance between taxa

Convert 3-d coordinates to 2-d probability simplex coordinates

Label vertices of 2-d probability simplex

Plot point in 2-d probability simplex

Draw 2-d probability simplex, with model lines for T3 or T1 model

Plot line segment in 2-d probability simplex

Add text at a point in 2-d probability simplex

Get all taxon names from a collection of trees