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pam
Purpose
Return a PAM scoring matrix
Syntax
ScoringMatrix = pam(N, 'PropertyName', PropertyValue)
[ScoringMatirx, MatrixInfo] = pam(N)
ScoringMatrix = pam(..., 'Extended', ExtendedValue)
ScoringMatrix = pam(..., 'Order', 'OrderValue')
Arguments
N
Enter values 10:10:500. The default ordering
of the output is A R N D C Q E G H I L K M
F P S T W Y V B Z X *.
Entering a larger value for N to allow sequence
alignments with larger evolutionary distances.
Extended
Order
Description
Property to add ambiguous characters to the
scoring matrix. Enter either true or false.
Default is false.
Property to control the order of amino acids
in the scoring matrix. Enter a string with at
least the 20 standard amino acids.
ScoringMatrix = pam(N, 'PropertyName', PropertyValue) returns
a PAM scoring matrix for amino acid sequences.
[ScoringMatrix, MatrixInfo] = pam(N) returns a structure with
information about the PAM matrix. The fields in the structure are Name,
Scale, Entropy, Expected, and Order.
B = pam(..., 'Extended', 'ExtendedValue') if Extended is true,
returns a scoring matrix with the 20 amino acid characters, the
ambiguous characters, and stop character (B, Z, X, *), . If Extended is
false, only the standard 20 amino acids are included in the matrix.
B = pam(..., 'Order', 'OrderString') returns a PAM matrix
ordered by the amino acid sequence in Order. If Order does not contain
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