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Last update on 13. Nov 2025 .
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    Track alignment changes

    OCCURRENCE

    ARB_NT/Sequences/Track alignment changes

     

    DESCRIPTION

    When run the first time, a checksum entry is created for every species that has data in the chosen alignment. For alignment 'ali_16s' the entry is named 'checksum_ali_16s'.

    On subsequent runs, stored checksums are compared with current checksums. If a checksum differs, a descriptive line is added to the 'seq_history' field for that species.

     

    NOTES

    Each 'checksum_xxx' entry stores two checksums:

    • the first checksum ignores gaps and reflects changes to sequence data
    • the second checksum includes gaps and reflects changes to the alignment

     

    EXAMPLES

    Use the following recommended workflow to track alignment and sequence changes:

    • Before starting an editing/alignment session, run 'Track changes' on the alignment you plan to work with and supply an identifier (for example your initials 'YN'). This records the baseline checksums.
    • Now edit your sequence data using the various aligners or the ARB sequence editor to adjust your alignment or eventually modify the sequence data itself.
    • After finishing, run 'Track changes' again and use a unique suffix such as 'YN-1'. This run compares checksums and adds lines to 'seq_history' for species whose checksums changed.
    • To find species affected by a particular session, search the 'seq_history' field with one of these expressions: 
      Description:                 /Search expression/
-                            -
alignment-only changes:      /YN-1 ali[^ ]* alignment changed/
sequence-data changes:       /YN-1 ali[^ ]* sequence changed/
newly imported species:      /YN-1 ali[^ ]* new/
      Replace 'YN-1' with your actual session identifier (many users prefer a date-based tag like 'YN-20250910').

    'Track changes' inserts a unique timestamp in each run, using the same timestamp for ALL entries updated in one run. You can use that timestamp for searching as shown in the following examples:

    Description:                 /Search expression/
-                            -
all changed by one session   *2025/09/10 12:46 YN ali_16s*
alignment-only changes       *2025/09/10 12:46 YN ali_16s alignment changed*

    Note: avoid using wildcards in the middle of expressions, they may match unintended text (found in older history lines).

     

    WARNINGS

    None

     

    BUGS

    No bugs known