What methods does MegAlign Pro offer for computing phylogeny?

MegAlign Pro offers two algorithms for generating phylogenetic trees:

• Neighbor joining: BIONJ uses the BIONJ algorithm (Gascuel, 1997, a variant of the Neighbor-Joining algorithm (Saito and Nei, 1987) that was used in classic MegAlign.
• Maximum likelihood: RAxML was developed by Alexandros Stamatakis (2014). Comprehensive information about options associated with this algorithm can be found in the RAxML Manual (PDF).

How do I create and compare multiple phylogenetic trees in my alignment project?

Following a multiple sequence alignment, you can create a phylogenetic tree by opening the Tree View and selecting the tree-building algorithm you wish to use.

To create an additional phylogenetic tree for comparison (using different parameters or after making changes to the alignment), click the green plus-sign tool, located at the top of the Tree View.

Can I apply bootstrapping to phylogenetic trees?

Yes, MegAlign Pro supports bootstrap analysis using the RAxML method for Maximum Likelihood trees. To perform bootstrapping, first perform an alignment and then create a Maximum Likelihood tree. In the RAxML options dialog, check the Bootstrap analysis checkbox. You can adjust the number of iterations and the seed to refine and reproduce bootstrap values.

Can I export my phylogenetic tree?

Yes. You can export your tree in either Newick or Nexus formats that are compatible with third part tree editing programs like FigTree by selecting File > Export Data > Tree.

You can also export an image of your phylogenetic tree in Adobe PDF (.pdf), Microsoft PowerPoint-optimized (.pptx), PNG image (.png) or JPG (.jpg, .jpeg) formats by selecting File > Export Image > Tree or clicking on the camera icon from the Tree view.