4.1 Color Table Settings.

4.1.1. Click menu/Align/Settings, and then click the “color table” option sheet.

Figure 4-1 Setting colors for each of the 64 codons

4.1.2. Locate the row of which you want to change the color, click the small button in “Current Color” column. Then select a new color and click the OK button to add the color you like into the color table.

4.1.3. If you want to apply current color settings, Click the “Save” button, your custom color settings will be saved. And your custom color settings will be loaded when you run CAUSA next time.

4.1.4. Select “Recover System Default” to restore all codon colors to default settings.

4.2 Alignment Settings.

Table 1. Optimal parameters for Clustalw to align combined DNA-Protein sequences

Option Parameter Description
-NEGATIVE ON protein   alignment with negative values in matrix
-PWMATRIX <CDP   file> User-defined pairwise   alignments scoring matrix
-PWGAPOPEN 20~40 Pairwise alignments   gap opening penalty
-PWGAPEXT 0.1~0.2 Pairwise alignments   gap extension penalty
-MATRIX <CDP   file> User-defined multiple   alignments scoring matrix
-GAPOPEN 20~40 Multiple alignments   gap opening penalty
-GAPEXT 0.2~0.5 Multiple alignments   gap extension penalty
-ENDGAPS NO No end gap   separation penalty.
-GAPDIST 4 Gap separation penalty   range

4.3 Matrix Settings

4.3.1. Click the “Matrix” button in the bottom of the alignment dialog to configure the scoring matrix.

Figure 4-2 Setting Scoring Matrix

4.3.2. You can select an existing matrix in the list box in the left bottom of the dialog. All existing matrixes will be saved in the directory [InstallDIR]\config\matrix.

4.3.3. To change a value of the scoring matrix, click the cell you want to change and type in a new score for the substitution.

4.3.4. Type in a new matrix name in the “Matrix Name”text box;

4.3.5. Click “Save” button to confirm and save your custom matrix settings.

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