The Split Sequence Set tool, located in the Other section of the Toolkit panel, separates multi-sequence files into multiple files, each consisting of a single sequence.

Note: Sequences that have been split may later be combined in a common file using the Collect Sequences tool.

  • This dialog requires you to select a sequence source. See Write to Results File for information on using the File, Sequence Text, Variable and Function buttons.
  • To specify the required filename pattern, click the Edit Pattern button. See Use File Patterns for detailed information.
  • If desired, enter a value in the Limit Files To box to limit the number of sequence files that can be generated during a run. The default is 1000.

If you have specified “full” file conversion, each sequence file that is generated may be accompanied by auxiliary files, as well.


The input file, 454Reads.fna, consists of 13 sequences in a multi-sequence file format.

After running the script, the first ten sequences in 454Reads.fna are saved as individual sequence files in .fasta format.

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