To set SeqVerter options:

• Select SeqVerter options from the Options menu.  This will call the SeqVerter options dialog box.
• The Options dialog box contains a tab control with five tabs:
  • Folders - sets the folders used to initialize the dialog boxes used in import and export operations.
  • Formats - sets the order that sequence file format names are presented in the export dialog boxes.
  • Dialogs - toggles the display of various dialog boxes.
  • Trace files - sets default options for trace file processing.
  • Alignments - sets default options for alignment file processing.
• Set options as required.
• Press OK.

Folders tab:
You can initialize import and export dialog boxes using default folders, or the last folder visited.

• Select Default folders to use SeqVerter's default folders.
• Select Last folder visited to use the last folder used for import or export.

The default folders may be set to use My Documents, or any other folder you enter.  To set the default folders:

• Select My Documents to use the folders created when SeqVerter is installed.
• Select Other to use the folders entered in the Import and Export fields.

Formats tab:
When sequences are exported, the file format is selected from drop-down lists.  The Formats tab allows you to order the list according to your own preferences.  To order the format lists:

• Press Merge sequences format list or Split sequences format list.  The Set format order dialog box will be displayed.
• A list of sequence formats is displayed.  Click on the name of the format you wish to move.
• Press Move up or Move down to change the position of the format name.
• Press OK to continue.

Dialogs tab:
SeqVerter displays many dialog boxes used to present options or information.  The display of these dialog boxes can be toggled using the Dialogs tab.  To toggle the display of a dialog box, click on the checkbox next to the dialog box name.

Note: When you hide a dialog box that presents options for a file operation, the default options will be applied.

Trace files tab:
When automatic sequencer trace files are exported, the sequence may be trimmed at the 5' and 3' ends.  The Trace file tab sets options that control trimming.
Set 5' end processing options:

• Select the Trim 5' end check box to enable 5' end processing.
• Enter a fixed cut-off position for in the Cut-off field 5' end trimming.

Set 3' end processing options:

• Select the Trim 3' end check box to enable 3' end processing.
• To use a fixed cut-off position, select the Fixed cut-off checkbox, and enter a position in the Cutoff field.
• To scan for an optimal cut-off position, select the Automated cut-off checkbox, and enter the desired Window size and number of N's to scan for.

Alignments tab:
Alignment file formats such as MSF, Nexus/PAUP, and PHYLIP require sequences to have the same length.  The Alignments tab provides options to process sequences exported to these formats.  Use the Padding options group to choose how the sequences will be made the same length:

• Select Pad sequences to add trailing blanks to lengthen shorter sequences to the length of the longest sequence.
• Select Truncate sequences to truncate longer sequences to the length of the shortest sequence.

Use the Alignment options group to control how the sequences are sized, and how gaps and non-sequence characters are handled.

• Select Remove empty alignment columns to remove columns that contain only gap characters.
• Select Remove columns with gaps to remove all columns that contain gaps.
• Select For nucleotide sequences, remove columns containing characters other than: A, C, G, C, U and gaps to remove columns containing ambiguous characters.

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