What methods does MegAlign Pro offer for computing phylogeny?
MegAlign Pro offers two algorithms for generating phylogenetic trees:
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 generate support values for a phylogenetic tree?
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.
Can I change the order of the sequences in my phylogenetic tree?
Yes. Options under the Tree menu give you the ability organize sequences on the phylogenetic tree by depth or distance, or to sort sequences in the alignment to reflect the order of sequences in the tree.
Can I change the order of the sequences in my phylogenetic tree?
Yes. Options under the Tree menu give you the ability organize sequences on the phylogenetic tree by depth or distance, or to sort sequences in the alignment to reflect the order of sequences in the tree.
Can I re-root my phylogenetic tree?
Yes. For purposes of visualization or publication, you may wish to root the tree or choose a different location for the root. For example, you may wish to balance the tree by moving the root to a long branch.
To re-root a tree, select Tree > Root On or click on the Sort Sequences button from the toolbar and use the Root On commands there.
Root On > Selected Branch places the root at the base of the currently selected branch.
Root On > Midpoint Branch computes the midway point between the two leaf nodes that are farthest apart and places the root there.
