circHybOrders: Generate all circular orders with designated hybrid

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

Generate all circular orders with designated hybrid

Description

Generate a matrix whose rows give all circular orders with a designated hybrid. The order is encoded as a vector with entries from 1 to n, where the position corresponds to a node/group of taxa. The location in the vector of the 1 indicates the hybrid, the positions of 2, n its neighbors, etc.

Usage

circHybOrders(n)

Arguments

n	size of order, with n>3

Details

To avoid duplication of circular orders, the entry 2 in each vector always occurs before the entry n.

Since in using first-order quartet-based methods to infer 4-cycles the hybrid node is not identifiable, for n=4 only 3 orders are given, with 1 as hybrid for each

Value

an (n!/2)xn (or 3xn if n=4) matrix whose rows give all circular orders.

Examples

circHybOrders(4)
circHybOrders(5)

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