quartetCutMLE: Maximum likelihood estimate of quartet tree of blobs topology...

In MSCquartets: Analyzing Gene Tree Quartets under the Multi-Species Coalescent

Maximum likelihood estimate of quartet tree of blobs topology and CF under Cut model

Description

Computes Maximum likelihood estimate of quartet tree of blobs topology and CF under the Cut model of \insertCiteABMR24;textualMSCquartets, Section 3. In case of ties, the topology and CF estimate are chosen randomly among those maximizing the likelihood. In particular, a resolved tree of blobs is always returned.

Usage

quartetCutMLE(qcCF)

Arguments

qcCF	a quartet count Concordance Factor (a 3-element vector)

Value

output with output$topology = 1, 2, or 3 indicating topology of tree of blobs in accord with ordering of qcCF entries, and output$CFhat the ML estimate for the CF

References

\insertRef

ABMR24MSCquartets

Examples

 quartetCutMLE(c(17,72,11))
 quartetCutMLE(c(48,11,41))
 quartetCutMLE(c(11,48,41))
 quartetCutMLE(c(48,41,11))

MSCquartets documentation built on Oct. 31, 2024, 1:08 a.m.