newMatrix.CodonSubst

CodonSubst.newMatrix

newMatrix,CodonSubst-method

name

paml.file

equ.dist

<p>New codon substitution matrix from PAML file.</p>

An extensible object-oriented framework for the Monte Carlo simulation of sequence evolution written in 100 percent R. It is built on the top of the R.oo and ape packages and uses Gillespie's direct method to simulate substitutions, insertions and deletions. Citation: Botond Sipos, Tim Massingham, Gregory E Jordan and Nick Goldman (2011) PhyloSim - Monte Carlo simulation of sequence evolution in the R statistical computing environment <doi:10.1186/1471-2105-12-104>.

Botond Sipos

phylosim

Flexible Simulations of Biological Sequence Evolution

newMatrix.CodonSubst function

New codon substitution matrix from PAML file — newMatrix.CodonSubst

New codon substitution matrix from PAML file

newMatrix.CodonSubst: New codon substitution matrix from PAML file

Description

Usage

Arguments

Value

See Also