MSCquartets3.0 package

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>.

Maintainer: John Rhodes License: MIT + file LICENSE Last published: 2024-10-30