SeqVerter allows you to set
options controlling every aspect of the program.
To set options:
- Press Options. This will call the 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
- Dialogs - toggles
the display of various dialog boxes.
- Trace files
- sets default options for trace file processing.
- sets default options for alignment file processing.
- Set options as required.
- Press OK.
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.
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.
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.
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.