Add gapped sequences to a project

To import gapped sequences from an existing MegAlign Pro file (.msa):

The following procedures both remove gaps from the sequences and place the updated sequences in the “Unassembled Sequences” area of the project.

• Click on the Add Sequences button ( ) or select File > Add Sequences and choose the .msa file.

• Use File > Open and choose the .msa file. Once the project is open, select all the sequences, then use Align > Unalign Selected.

*Note : MegAlign Pro uses a dash (-) to represent gaps. MegAlign Pro does accept sequences where gaps are represented by letters such as “n” or “x.” Sequences with non-IUPAC symbols other than dashes may be accepted by MegAlign Pro as input, but may not be recognized by certain alignment algorithms. Of MegAlign Pro’s methods, MAFFT is the most tolerant of non-IUPAC symbols.

To import gapped nucleotide sequences from another type of file (not .msa):

When the gapped sequences are not part of a MegAlign Pro file, you can use SeqMan Pro to remove the gaps. This procedure is safe to use for nucleotide (DNA or RNA) sequences only.

1. Launch DNASTAR SeqMan Pro, then drag and drop the gapped sequence file(s) onto the SeqMan Pro window.

2. Select all sequences in the Unassembled Sequences using Ctrl+A (Win) or Cmd+A (Mac).

3. Use Contig > Export Sequences > Single File.

4. Select either FastA or GenBank Flat File format and choose a file name and location. Make sure that Include gaps is left unchecked, and then click Save.

The sequence(s) in the newly saved file can now be added in the usual way.

!WARNING: Do not use this method for protein sequences, as all letters that are not also in the IUPAC nucleic acid code will be lost.