Exporting sequences to alignment file formats

Alignment file formats such as MSF, Nexus/PAUP, and PHYLIP require sequences to have the same length. SeqVerter provides options to process sequences exported to these formats that control how the sequences are sized, and how gaps and non-sequence characters are handled.

To export sequences to alignment file formats:

  • Select sequences for export by clicking the checkbox next to the sequence name, or press Select all to export all open sequences.
  • Press Merge sequences.  The standard windows Save as dialog box will be displayed.
  • Enter a name for the saved file in the File name field.
  • Choose the alignment file format from the File format list.
  • Choose the desired operating system from the OS Targets drop down list.
  • Press OK to continue.  The Alignment processing dialog box will be displayed.
  • Use the Padding options group to choose how the sequences will be made the same length (required by many sequence alignment and phylogeny reconstruction programs):
    • 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 non-ambiguous characters.
  • Press OK to continue.  A summary of the file operation will be displayed in the Export results dialog box.

If the Alignment processing dialog box is not displayed, you can enable it using the Dialogs tab in the Options dialog box.  See Setting options for more information.
For more information on formats, please read the 'Sequence file format notes'