How do I export my sequence or alignment as formatted text?

In Geneious Prime 2019.1 onwards the Text View tab is able to display your sequences or alignments in a customisable rich text or plain text format which can then be exported or copied and pasted into a text or Microsoft Word document.  

To use this new feature, select a sequence or an alignment and switch to the Text View pane.

Single sequences

Use the Sequence format: dropdown menu to select whether to view in CustomGenBank, or original plain view (Don't reformat).

sequence_display_text.png

Use the Display options button to show the Formatting Options dialog window and choose to display in plain text or rich text format and set font sizes for rich text. 

You can also choose to display the reverse strand by checking Reverse complement, and/or choose to Show translation on a selected frame.

Under Layout, you can choose the number of characters per line, margin width and ruler settings.

If you choose rich text format, then you can also use the  Sequence colors option to highlight one or more regions in the sequence or alignment with color.

sequence_formatting.png

 

Alignments

Use the Customize format: dropdown menu to display the Custom view or the original plain view (Don't reformat).

text_formatting.png

 Use the Display options button to show the Formatting Options dialog window and choose to display in plain text or rich text format.  

The Highlight bases section allows you to show disagreements, agreements, similarities and dissimilarities to the Consensus or Reference sequence, with non-highlighted bases displayed as dots.  If this setting is off, differences from the Consensus or Reference are displayed as lowercase bases.  If this setting is on, and Disagreements or Similarities is chosen, similar bases are shown in lower case (for nucleotide sequences, ambiguities are regarded as similarities).  For more information on scoring matrices used to calculate identities and similarities, see the section on Command Line Arguments (specifically -matrix, and -similarcase) at this link

You can also set the Layout and Sequence Colors in the same way as for a single sequence. 

display_options.png

 

Exporting your formatted text

Use the Copy full sequence button to copy the displayed text to the clipboard, or use the Save as*.txt button to export the displayed text as a text file.

 

 

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