static MD()
{
matrices.Add("MD40", SubstitutionMatrix.Create("MD40", MatrixData.MD40, Routines.aminoAcidCodes));
matrices.Add("MD120", SubstitutionMatrix.Create("MD120", MatrixData.MD120, Routines.aminoAcidCodes));
matrices.Add("MD250", SubstitutionMatrix.Create("MD250", MatrixData.MD250, Routines.aminoAcidCodes));
matrices.Add("MD350", SubstitutionMatrix.Create("MD350", MatrixData.MD350, Routines.aminoAcidCodes));
}
static PAM()
{
matrices.Add("PAM20", SubstitutionMatrix.Create("PAM20", MatrixData.PAM20, Routines.aminoAcidCodes));
matrices.Add("PAM60", SubstitutionMatrix.Create("PAM60", MatrixData.PAM60, Routines.aminoAcidCodes));
matrices.Add("PAM120", SubstitutionMatrix.Create("PAM120", MatrixData.PAM120, Routines.aminoAcidCodes));
matrices.Add("PAM160", SubstitutionMatrix.Create("PAM160", MatrixData.PAM160, Routines.aminoAcidCodes));
matrices.Add("PAM250", SubstitutionMatrix.Create("PAM250", MatrixData.PAM250, Routines.aminoAcidCodes));
matrices.Add("PAM350", SubstitutionMatrix.Create("PAM350", MatrixData.PAM350, Routines.aminoAcidCodes));
}
static Gonnet()
{
matrices.Add("Gonnet40", SubstitutionMatrix.Create("Gonnet40", MatrixData.Gonnet40, Routines.aminoAcidCodes));
matrices.Add("Gonnet80", SubstitutionMatrix.Create("Gonnet80", MatrixData.Gonnet80, Routines.aminoAcidCodes));
matrices.Add("Gonnet120", SubstitutionMatrix.Create("Gonnet120", MatrixData.Gonnet120, Routines.aminoAcidCodes));
matrices.Add("Gonnet160", SubstitutionMatrix.Create("Gonnet160", MatrixData.Gonnet160, Routines.aminoAcidCodes));
matrices.Add("Gonnet250", SubstitutionMatrix.Create("Gonnet250", MatrixData.Gonnet250, Routines.aminoAcidCodes));
matrices.Add("Gonnet300", SubstitutionMatrix.Create("Gonnet300", MatrixData.Gonnet300, Routines.aminoAcidCodes));
matrices.Add("Gonnet350", SubstitutionMatrix.Create("Gonnet350", MatrixData.Gonnet350, Routines.aminoAcidCodes));
}
static BLOSUM()
{
matrices.Add("BLOSUM30", SubstitutionMatrix.Create("BLOSUM30", MatrixData.BLOSUM30, Routines.aminoAcidCodes));
matrices.Add("BLOSUM35", SubstitutionMatrix.Create("BLOSUM35", MatrixData.BLOSUM35, Routines.aminoAcidCodes));
matrices.Add("BLOSUM40", SubstitutionMatrix.Create("BLOSUM40", MatrixData.BLOSUM40, Routines.aminoAcidCodes));
matrices.Add("BLOSUM45", SubstitutionMatrix.Create("BLOSUM45", MatrixData.BLOSUM45, Routines.aminoAcidCodes));
matrices.Add("BLOSUM50", SubstitutionMatrix.Create("BLOSUM50", MatrixData.BLOSUM50, Routines.aminoAcidCodes));
matrices.Add("BLOSUM55", SubstitutionMatrix.Create("BLOSUM55", MatrixData.BLOSUM55, Routines.aminoAcidCodes));
matrices.Add("BLOSUM62", SubstitutionMatrix.Create("BLOSUM62", MatrixData.BLOSUM62, Routines.aminoAcidCodes));
matrices.Add("BLOSUM62x2", SubstitutionMatrix.Create("BLOSUM62x2", MatrixData.BLOSUM62x2, Routines.aminoAcidCodes));
matrices.Add("BLOSUM65", SubstitutionMatrix.Create("BLOSUM65", MatrixData.BLOSUM65, Routines.aminoAcidCodes));
matrices.Add("BLOSUM70", SubstitutionMatrix.Create("BLOSUM70", MatrixData.BLOSUM70, Routines.aminoAcidCodes));
matrices.Add("BLOSUM75", SubstitutionMatrix.Create("BLOSUM75", MatrixData.BLOSUM75, Routines.aminoAcidCodes));
matrices.Add("BLOSUM80", SubstitutionMatrix.Create("BLOSUM80", MatrixData.BLOSUM80, Routines.aminoAcidCodes));
matrices.Add("BLOSUM90", SubstitutionMatrix.Create("BLOSUM90", MatrixData.BLOSUM90, Routines.aminoAcidCodes));
}
static IUB() // Also referred to as SW_GAP in Clustal code
{
matrix = SubstitutionMatrix.Create("IUB", MatrixData.IUB, Routines.nucleotideCodes);
}
static AminoAcidIdentity()
{
matrix = SubstitutionMatrix.Create("Identity", MatrixData.AminoAcidIdentity, Routines.aminoAcidCodes);
}
static NucleotideIdentity() // Also referred to as ClustalVDNA in Clustal code, or ClustalW (1.6)
{
matrix = SubstitutionMatrix.Create("Identity", MatrixData.NucleotideIdentity, Routines.nucleotideCodes);
}