MegAlign Pro Product Notifications

MegAlign Pro

After installing Lasergene on Windows, antivirus programs may report “Shellshock” vulnerability

Date: 10/8/2014


Version Affected: 12.0 and higher


Version Fixed: N/A


Issue: To support MegAlign’s MAFFT alignment algorithm, the Windows version of Lasergene installs and uses a version of GNU Bash containing the recently published ShellShock vulnerability. Antivirus programs may flag this as a risk.


The GNU Bash installed by Lasergene is not exposed to external attackers, as it is installed for use only by MegAlign Pro. It is not used by web servers or other known attack vectors. Therefore, we believe that Lasergene installation poses no risk to our customers.


ShellShock vulnerability is described further on the U.S. CERT website.


Note: This issue does not affect Macintosh installations of Lasergene.


Resolution: We are actively working toward updating GNU Bash in a future release of Lasergene.


If desired, you may remove this version of GNU Bash from the MegAlign Pro installation. Doing so will make the MAFFT alignment engine unavailable until you perform a new Lasergene installation. For assistance in removing GNU Bash, contact DNASTAR at 866-511-5090 or


Clustal Omega alignment does not complete and results in a “fatal error” message

Date:   6/17/2014


Version Affected:  11.2 and higher


Version Fixed:  N/A


Issue:  Clustal Omega requires that each sequence in an alignment contain at least one residue that is not an ambiguity code.




  • DNA sequences must contain at least one A, C, T or G.
  • RNA sequences must contain at least one A, C, U, or G.
  • Protein sequences must contain at least one A, C, D, E, F, G, H, I, K, L, M, N, P, Q, R, S, T, V, W or Y.


If there are any sequences that do not meet this requirement, Clustal Omega will terminate with a “fatal error” message (visible in the MegAlign Pro Console), and no alignment will be created.


To address this issue, you can do either of the following:


  • Remove the sequence and try aligning again with Clustal Omega.
  • Include the sequence, but switch to MAFFT or MUSCLE as the alignment method. Neither of these algorithms requires sequences to contain at least one non-ambiguous residue.


If you have any questions about this issue, please contact DNASTAR by calling 866-511-5090 or by e-mailing us at


MUSCLE gives similar, but not identical, alignment results on Windows and Macintosh

Date:   4/20/2013


Version Affected:  11.0 and later


Version Fixed:  N/A


Issue:  Performing an identical MUSCLE alignment on the two platforms yields correct results on both platforms, but the results may not be identical to one another.


Resolution: This discrepancy may be due to a slight difference in the number of iterations used during assembly.


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