Analyzing Gene Tree Quartets under the Multi-Species Coalescent
Generate permutations
Compute empirical distance between taxon groups.
Main loop of B-quartet inference
Generate all circular orders with designated hybrid
Collapse short tree edges
Combine several cycle resolutions on a tree of blobs to create a netwo...
Extract compatible splits
Probability density function for Cut Model
Simulated gene tree dataset from species tree
Papionini 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 tr...
Expected modNANUQ cycle distance
Expected NANUQ cycle distance
Compute fit of circular orders to distance with least squares
Apply Holm-Bonferroni method to adjust for multiple tests
Initialize vector of B quartets
Label internal nodes on tree
Modified Struve function
Multispecies Coalescent Model Quartet Package
Apply NANUQ network inference algorithm to gene tree data
Compute NANUQ distance and write to file
Write a distance table to a file in nexus format
Groups taxa by deleting a node in a tree
Choose cycle orders heuristically from empirical modNANUQ distance
Power divergence statistic of Cressie & Read
Plot histogram of log p-values in table
Compute Quartet Distance Consensus tree from gene tree data
Compute Quartet Distance Supertree
Produce simplex plot with results of B/T-quartet inference
Maximum likelihood estimate of quartet tree of blobs topology and CF u...
Hypothesis test for quartet counts fitting a resolved quartet tree of ...
Multiple independent hypothesis tests for quartet counts fitting the C...
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 ...
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 le...
Produce table of counts of quartets displayed on trees, in parallel fo...
Print a quartet table with nice formatting
Modify quartet table to show only resolved quartets
Build quartet table from distances
Produce simplex plot with results of quartet hypothesis tests
Bayesian posterior probability of error in 4-taxon unrooted species tr...
Hypothesis test for quartet counts fitting a tree under the MSC
Multiple independent hypothesis tests for quartet counts fitting a spe...
Compute the Weighted Quartet Distance between taxa
Resolve a node on a tree of blobs as a cycle
Resolve Tree of Blobs to Level-1 network
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
Sort quartet table rows by lex order
Probability density function for Model T1
Probability density function for Model T3
Get all taxon names from a collection of trees
TINNIK algorithm to infer species tree of blobs
Compute TINNIK distance from quartets and hypothesis test p-values
Topological distances on a tree
Produce tree from compatible splits
Tree of blobs for a network
Compute Weighted Quartet Distance Consensus tree from gene tree data
Compute the Recursive Weighted Quartet Distance Consensus tree from ge...
Compute the Weighted Quartet Distance Supertree
Adjust edge lengths on tree built from Weighted Quartet distance to es...
Methods for analyzing and using quartets displayed on a collection of gene trees, primarily to make inferences about the species tree or network under the multi-species coalescent model. These include quartet hypothesis tests for the model, as developed by Mitchell et al. (2019) <doi:10.1214/19-EJS1576>, simplex plots of quartet concordance factors as presented by Allman et al. (2020) <doi:10.1101/2020.02.13.948083>, species tree inference methods based on quartet distances of Rhodes (2019) <doi:10.1109/TCBB.2019.2917204> and Yourdkhani and Rhodes (2019) <doi:10.1007/s11538-020-00773-4>, the NANUQ algorithm for inference of level-1 species networks of Allman et al. (2019) <doi:10.1186/s13015-019-0159-2>, the TINNIK algorithm for inference of the tree of blobs of an arbitrary network of Allman et al.(2022) <doi:10.1007/s00285-022-01838-9>, and NANUQ+ routines for resolving multifurcations in the tree of blobs to cycles as in Allman et al.(2024) (forthcoming). Software announcement by Rhodes et al. (2020) <doi:10.1093/bioinformatics/btaa868>.