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CreateOrigDayMatrix

Function CreateOrigDayMatrix

Calling Sequence CreateOrigDayMatrix(Mutations,AaCounts,PamNumber)
CreateOrigDayMatrix(mutations,counts,1..UpperPam)

Parameters

Name	Type	Description

`Mutations`	array(numeric,20,20)
`AaCounts`	array(numeric,20)
`PamNumber`	numeric

Return Type {DayMatrix,list(DayMatrix)}

Synopsis This function computes a Dayhoff matrix (structured type DayMatrix) computed by the method first given by Dayhoff et. all cite{DayhoffOS78} given an observed mutation matrix mutations, a frequency vector counts and a PAM distance PAM (or range of PAM distances beginning at 1).

Examples

> OrigTot := [87, 41, 40, 47, 33, 38, 50, 89, 34, 37,85, 81, 15, 40, 51, 70, 58, 10, 30, 65];

OrigTot := [87, 41, 40, 47, 33, 38, 50, 89, 34, 37, 85, 81, 15, 40, 51, 70, 58, 
10, 30, 65]

> OrigFreq := OrigTot/sum(OrigTot);

OrigFreq := [0.08691309, 0.04095904, 0.03996004, 0.04695305, 0.03296703, 0.03796
204, 0.04995005, 0.08891109, 0.03396603, 0.03696304, 0.08491508, 0.08091908, 0.0
1498501, 0.03996004, 0.05094905, 0.06993007, 0.05794206, 0.00999001, 0.02997003,
 0.06493506]

> OrigDM := CreateOrigDayMatrix(Mutations1978, OrigFreq, 250);

OrigDM := DayMatrix(Peptide, pam=250, Sim: max=17.302, min=-7.510, del=-19.814-1
.396*(k-1))

See also CreateDayMatrices, CreateDayMatrix, DayMatrix, SearchDayMatrix