By now you may have heard that DNASTAR will be retiring MegAlign with the Lasergene 16 release in summer of 2019. What does this change mean for you and your colleagues that are still using the popular multiple sequence alignment application? And what can you do to prepare for the change?
…Hello MegAlign Pro!
Over the past few years, DNASTAR has been working towards standardizing and modernizing our user graphical user interfaces (GUIs). Part of the rationale behind this change was to make our software nicer looking, more intuitive, and consistent between our applications. In addition, we wanted to provide our users access to the most current and powerful 64-bit alignment algorithms .
The new style interface began with Protean 3D, which replaced our 32-bit classic application Protean. With Protean 3D, we introduced 3D protein structure visualization and analysis, along with the classic sequence-based analysis methods from Protean. Following on the success of Protean 3D, a series of new programs with the new-style interface were introduced: DNASTAR Navigator, SeqNinja, GenVision Pro, and MegAlign Pro. The first three applications had no existing counterparts within the DNASTAR Lasergene package, so there was no real transition involved for users.
MegAlign Pro, which was first introduced in Lasergene 11, is the replacement for the original 32-bit MegAlign. As with Protean/Protean 3D, transition from MegAlign to MegAlign Pro involved new functionality as well as a new look and feel.
New methods for multiple alignment and pairwise alignment
The most important new functionality in MegAlign Pro is the inclusion of a set of more modern multiple alignment engines, specifically MUSCLE, MAFFT, Clustal Omega and the remarkable genome aligner, Mauve. MegAlign Pro also retains the venerable but still-popular aligner ClustalW2.
MegAlign’s pairwise alignment algorithms, Wilbur-Lipman, Martinez-NW and Lipman-Pearson, have been replaced with MegAlign Pro’s more standard Needleman-Wunsch and Smith-Waterman algorithms for global, semi-global and local alignment. These are fast and relatively high-capacity pairwise aligners which use hardware acceleration where possible. To learn more about pairwise alignment in MegAlign Pro, check out our new pairwise alignment tutorials.
MegAlign Pro is still transitional and we are continuing to add more of the original MegAlign functionality with each release. For example, Lasergene 16 will allow you to search NCBI’s BLAST and Entrez databases from within MegAlign Pro, Protean 3D and GenVision Pro. In the near future, we also intend to recreate MegAlign’s editing capabilities in MegAlign Pro
Why change a good thing?
We know that many of you are still using original MegAlign. However, upcoming changes announced for our supported operating systems will make it impossible to continue distributing these “classic” applications. For instance, the Catalina macOS update to be released in Fall 2019 will not support the classic 32-bit Lasergene applications, all of which have been superseded by more modern Lasergene applications
How to make the switch
We understand that change isn’t always easy, so we’ve prepared a new User Guide just for you. The guide explains how to transition from MegAlign to MegAlign Pro with detailed steps and images comparing the two applications. If you happen to be a user of EditSeq or PrimerSelect—also retiring in Lasergene 16.0—this guide also explains how to transition from those apps to SeqBuilder Pro.