MegAlign Pro lets you filter a set of sequences and then apply or keep only those that meet your specified criteria.

Use the Filter results tool () to launch the Filter Sequences dialog. This dialog lets you limit matches in the table by setting up custom filters.

To launch the Filter Sequences dialog:

Use any of the following methods:

  • From the Welcome screen, select New Project on the left and Filter and align sequences on the right.
  • Within any project, choose File > Add Sequences with Filter.
  • Within any project, press the black triangle to the right of the Add Sequences to Project tool () and choose Add Sequences with Filter.
  • After searching NCBI’s BLAST or Entrez databases, press the Filter results tool () in the header above the Table view and then choose Filter.


To set up the filters:

  1. If prompted, select one or more sequences or a folder of sequences from the file picker and click Open. This step is skipped if you are filtering search results, as MegAlign Pro will be using the sequence matches from the table.
  1. The Filter or Filter Sequences dialog opens. Press the <select> drop-down menu to choose from among some of the filter types below. Available options depend on the circumstances under which you accessed the filter dialog.
Filter type Filters sequences to allow only sequences…
Accession Matching a particular Accession number.
Ambiguous residues With more or less than the desired number/percent of ambiguous residues.
% Coverage Where a specified portion of that sequence aligns to a match in the database.

Example: Query has 596 bases, of which 565 align to a match in the NCBI database. %Coverage = 565/596 = 95%.
Description Whose definition matches NCBI “Definition” field text.
% Identity Where a specified percentage of bases align to a match in the database. (NCBI definition).

Example: Query has 565 bases that align to the match and 3 bases that don’t match. %Identity = 562/565 = 99.5%.
Score Meeting the similarity score criteria for the match. (See the NCBI definition for raw score). In general, a higher score denotes a better match.
E-value That are not likely to match only coincidentally. (See the NCBI definition for E value). In general, a lower score denotes a better match.
Length Matching a specified length in base pairs.
Organism Matching a specified species name.
Probability Meeting criteria based on probability of inclusion.
Sequence Having a particular string of amino acids or nucleotides, with options to set the maximum number of mismatches or specify that the string can be found on either strand.
Sequence length Shorter or longer than a specified length.
Sequence name Having/lacking a certain string of letters/numbers in their names. Wildcards are supported.
Sequence number Incling only every ‘n’ number of sequences between two specified sequences, where ‘n’ is entered as the Interval.
  1. A variety of text or number boxes and additional drop-down menus will populate to the right of your selection. Enter the desired criteria for that filter row. The image below shows an example with two filter rows.

  1. To add another filter row, press the plus icon (). To delete a filter row, press the minus icon ().
  1. Once you have set up all desired filter rows, go to the top of the dialog and choose whether to Match all of the following or Match any of the following queries.
  1. After you finish setting up filters, do any of the following:

    • To apply the filters and open the sequences that met the criteria, press Apply or Filter.

    • To add all sequences without filtering, press Don’t Filter. This option is not available when filtering BLAST or Entrez matches.

    • To clear all filters and start over, press Clear or Clear Filter.

    • To exit the dialog without filtering, press Cancel.

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