Darwin Help

CreateCodonMatrices

Function CreateCodonMatrices - creates a global list of codon mutation matrices.

Calling Sequence CreateCodonMatrices()
CreateCodonMatrices(setname)
CreateCodonMatrices(counts)
CreateCodonMatrices(rates,freqs)

Parameters

Name	Type	Description

`setname`	string	Name of the desired set of species.
`count`	matrix(numeric)	Matrix with codon mutation counts.
`rates`	matrix(numeric)	a rate matrix Q
`freqs`	array(nonnegative)	codon frequencies

Return Type NULL

Globals AF, CF, CM, CMS, CodonLogPAM1, DM, DMS, logPAM1,

Synopsis When called with a set name, the precomputed logarithm of the respective mutation matrices are loaded and used to create the global scoring matrices. When called with no argument, the matrices are cretaed from the data form the OMA project. Alternatively, 'mt' can be used as setname to construct matrices for mitochondiral coding DNA. When a count matrix is given, the mutation matrices are derived from this matrix. When a rate matrix and the natural frequencies are given, then those are used to create the scoring matrices. The function creates the following global objects:

CF - a vector of length 64 containing the codon frequencies,

CodonLogPAM1 - the logarithm of a 1-CodonPAM mutation matrix,

CM - the 250-CodonPAM similarity matrix and

CMS - a list of 1266 similarity matrices.

Examples

> CreateCodonMatrices();

> CreateCodonMatrices(hum);

See also CreateDayMatrices, CreateSynMatrices