Viewing and formatting sequences with Pretty view

The Pretty viewer provides a printable, formatted view of sequences.  It can also be used to copy or save the display in RTF format for use in a word processor.  The Pretty viewer presents a display of the sequences in the Sequence Selection List, optionally displaying sequence numbering and base coloring.  Parameters affecting how the alignment is displayed can be accessed through the Viewers toolbar.

To view sequences in the Pretty viewer:

  • If the Viewers pane is hidden, make it visible by pressing the Viewers button in the main toolbar.
  • To view the alignment using Pretty, select the Pretty tab in the Viewers pane.

Formatting the Pretty display using the toolbar:

  • The line length is set using the Line length up and down arrows.
  • The character case is selected using the Case drop-down list.  The case can be left as it is, or can be set to upper or lower case.
  • The Coloring drop-down list is used to select the base coloring option.  The coloring can be set to none character coloring (black bases on white background), base colors (different color for each base - selectable in Options/Global options), or mean-pair score alignment shading.
  • The Font button allows you to set the font used for the display of the alignment.  Only fixed pitch fonts (monospaced) are valid entries.

Formatting the Pretty display using the Settings dialog box:

  • Line metrics/Length option sets the number of sequence characters displayed on each line.
  • Line metrics/Name width option controls the number of sequence name characters displayed.
  • Group in blocks causes a space to be inserted in the alignment at Block size intervals.
  • Numbering options control the placement of sequence position numbers.
  • Case options allow you to choose the character case used.
  • Replace matches to the first sequence with a dot (.) checkbox toggles the replacement of characters that match the character at the same position in the first sequence with a dot.

Importing the display into a word processor:

  • Press the Copy button on the toolbar.  This places the alignment display onto the Windows clipboard in RTF format for pasting into your word processor or presentation software.
  • Alternatively, press the Save button to save the alignment in an RTF file.  The file can be imported into word processors on any platform that supports the RTF format.

Printing the display:

  • The Print button sends the alignment to your printer.
  • The Print preview button allows you to preview the printed version.