To add standard (ungapped) sequences, or additional sequences, to an existing project:

You can add standard DNA, RNA or protein sequences from a wide variety of file types, including SeqNinja .star files. (See Advantages of using SeqNinja files).

  • Choose File > Add Sequences, select the Add Sequences button (), or press Ctrl/Cmd+E. Then choose one or more sequences from the file browser.
  • Drag & drop one or more sequence files (but not folders or MegAlign Pro .msa projects) on an open project.

A project can consist of any combination of file types, including single and multi-segment sequences, but all sequences must be either DNA, RNA or protein.


The following table shows error messages that you might encounter when adding sequences to a project.

Situation Message and response
Adding a MegAlign Project (.msa file)

Click OK to add unaligned sequences from the saved project to the current project. This is one way to remove gaps from sequences so that they can be used in MegAlign Pro.
Adding a sequence that contains gap characters (e.g., dashes or question marks)

Click OK to add only those sequences without gaps to the project. (There is a separate method for adding gapped sequences).
Attempting to enter mixed sequence types (both protein and nucleotide) to the Sequences View

Click OK to add all the sequences to the project. Afterwards, manually remove any sequences that are not of the desired category.
Attempting to load more than 1000 sequences Initial warning:



After clicking OK, a progress bar is displayed:



Press OK to continue loading all of the sequences. MegAlign Pro will display a progress bar (see lower image, left) with a running count of the number of sequences loaded so far. At any point, you may cancel the entire sample upload by pressing Cancel. This terminates the entering step without adding the new file(s). Otherwise, simply wait for the samples to finish loading.
Entering SeqNinja projects (.star) or FASTA files with ambiguous extensions (e.g., .fasta)

MegAlign Pro can usually determine whether the sequence consists of DNA, RNA or protein. If it cannot, MegAlign Pro will prompt you to specify file type by selecting a button from the dialog.
Attempting to add a SeqNinja project (.star) that contains errors

Click OK. Launch SeqNinja, fix any errors in the project and save it before adding the file to MegAlign Pro.

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