NRooted: Number of rooted/unrooted trees These functions return the...

In ms609/ProfileParsimony: Phylogenetic Inference by Profile Parsimony

Description

Functions starting N return the number of rooted or unrooted trees, functions starting Ln provide the log of this number. Calculations follow Carter et al. 1990, Theorem 2.

Usage

NRooted(tips, extra = 0)

NUnrooted1(tips, extra = 0)

LnUnrooted1(tips, extra = 0)

LnRooted(tips, extra = 0)

LnUnrooted(splits)

NUnrooted(splits)

LnUnrootedMult(splits)

NUnrootedMult(splits)

Arguments

tips	The number of tips.
extra	the number of points at which another branch cannot be added.
splits	vector listing the number of taxa in each tree bipartition.

Functions

• NUnrooted1: Number of unrooted trees

• LnUnrooted1: Log Number of unrooted trees

• LnRooted: Log Number of rooted trees

• LnUnrooted: Log number of unrooted trees

• NUnrooted: Number of unrooted trees

• LnUnrootedMult: Log unrooted mult

• NUnrootedMult: Number of unrooted trees (mult)

Author(s)

Martin R. Smith

References

Carter, M., Hendy, M., & Penny, D. (1990). On the distribution of lengths of evolutionary trees. SIAM Journal on Discrete Mathematics, 3(1), 38-47. doi: 10.1137/0403005

CARTER, M., HENDY, M., PENNY, D., SZEKELY, L. A. and WORMALD, N. C. 1990. On the distribution of lengths of evolutionary trees. SIAM Journal on Discrete Mathematics, 3, 38–47.

Examples

  NRooted(10)
  NUnrooted(10)
  LnRooted(10)
  LnUnrooted(10)
  # Number of trees consistent with a character whose states are 00000 11111 222
  NUnrootedMult(c(5,5,3))

ms609/ProfileParsimony documentation built on May 23, 2019, 7:49 a.m.