ordersHeuristicmodNANUQ: Choose cycle orders heuristically from empirical modNANUQ...

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

Choose cycle orders heuristically from empirical modNANUQ distance

Description

Find candidates for best hybrid node and circular order fitting the modNANUQ distance.

Usage

ordersHeuristicmodNANUQ(M, delta = 10^-6)

Arguments

M	an empirical modNANUQ distance table
delta	cutoff for relative difference in distances for determining near ties for "best" orders

Details

Candidadte orders are obtained by first picking the hybrid node (from the minimum column sum of the distance matrix), then ordering nodes by distance from the hybrid, and for each consecutive pair picking nodes in the cycle closest to the previous node. This constructs one or more orders since ties may occur. For more details, see \insertCiteABRW24;textualMSCquartets.

This function is used by NANUQ+ commands to resolve multifurcations in a tree of blobs of high degree.

Value

a list of circular orders

References

\insertRef

ABMR24MSCquartets

See Also

expmodNANUQCycleDist resolveCycle resolveLevel1

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