MatrixToPhyDat

matrix of tokens, probably created with <a rd-options="" href="/link/ReadCharacters?package=TreeSearch&version=0.3.2" data-mini-rdoc="TreeSearch::ReadCharacters">ReadCharacters</a>
or <a rd-options="" href="/link/ReadTntCharacters?package=TreeSearch&version=0.3.2" data-mini-rdoc="TreeSearch::ReadTntCharacters">ReadTntCharacters</a>.

tokens

Converts a matrix of tokens to a phyDat object

internal

Searches for phylogenetic trees that are optimal using a user-defined criterion.
Implements Profile Parsimony (Faith and Trueman, 2001) <doi:10.1080/10635150118627>, and
Successive Approximations (Farris, 1969) <doi:10.2307/2412182>.
Handles inapplicable data using the algorithm of Brazeau, Guillerme and Smith
(2019) <doi:10.1093/sysbio/syy083>.

Martin R. Smith

TreeSearch

Phylogenetic Tree Search Using Custom Optimality Criteria

Emmanuel Paradis

Klaus Schliep

Martin Brazeau

MatrixToPhyDat function

matrix of tokens, probably created with <a rd-options='' href='ReadCharacters'>ReadCharacters</a>
or <a rd-options='' href='ReadTntCharacters'>ReadTntCharacters</a>.

MatrixToPhyDat: Matrix to phydat

Description

Usage

Arguments

Value