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Last update on 06. Aug 2022 .
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Split sequences


ARB_NT/Sequence/Split sequences



Allows to split an alignment into multiple alignments.

One usecase of this function is to

  1. split an alignment into multiple partial alignments (parts)
  2. operate on single parts only (e.g. using an aligner)
  3. join the (modified) parts into the original alignment using ´Concatenation of sequences´.

Insert the "Target alignment prefix". This string will be appended by digits and then gets used as names of the generated partial alignments.

Insert a list of positions (comma-separated). The source alignment will be split before each of the given positions and the splitted sequence parts will be written into separate target alignments.

The easiest way to select positions to split is to
  • highlight a block in the arb sequence editor and
  • then click "Use editor range".

Choose whether all or only marked sequences should get splitted.

You may choose to overwrite existing alignments. This will completely delete these alignments and the stored data for any species or SAI w/o further confirmation.



When reducing the number of split positions while using the option to overwrite existing alignments, unused/unwanted alignments may remain. Consider using DELETE from ´Alignment Administration´ manually in that case.

The comment attached to each alignment does contain information about source, time and parts of each performed split, i.e. you may use the comment to decide whether alignments were generated in one split or are relicts from earlier splits.


SAI handling  

SAI data is handled more diversely:

  • when data is considered to be alignment relative, arb splits its contents into single partial alignments.
  • otherwise the content gets prefixed by the tag '[splitted]'.
  • some entries like 'FREQUENCIES' are not transferred. A placeholding comment is inserted into the target alignment instead.

SAIs like 'HELIX' are most likely functionally broken after splitting the alignment.









No bugs known