Phylogenetic Trees

After performing a multiple or pairwise alignment, a default phylogenetic tree appears in the Tree view. This tree is built using the currently-selected Distance metric and the Neighbor joining: BIONJ algorithm, which is described below. Additional trees can be generated for the alignment using the same or different algorithms. You can then use the Style panel’s Tree section to customize each tree as desired.

To generate a new tree:

1. Add sequences and create a multiple alignment. The default tree (named “Tree”) is created using the BIONJ algorithm.

2. Either choose Tree > Compute Phylogeny; or choose View > Explorer or press the Explorer tab to open the Trees section of the Explorer panel. Then press the green plus-sign tool () to the right of the table. In either case, the following dialog pops up.
   
   
   
   
   • Type in a new Name for the tree or keep the default name of Tree <number>.
     
     
   • From the Using menu, choose the desired method. MegAlign Pro supports two tree building algorithms: 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. This is the method MegAlign Pro uses to create the default phylogenetic tree. Maximum likelihood: RAxML was developed by Stamatakis (2014). Comprehensive information about options associated with this algorithm can be found in the RAxML Manual (PDF). If you choose Neighbor joining: BIONJ, skip to Step 4, below. Otherwise, continue to Step 3.

3. If you chose Maximum likelihood: RAxML, the dialog changes to display additional options. For information on these options, refer to the RAxML Manual.
   
   
   
   
   
   • Add a checkmark next to Bootstrap analysis to add a bootstrapping step to the calculation. If you add a checkmark, another option will appear. Type in the number of Iterations or keep the default value of 100.
     
     
   • Keep the default Seed value, type in a new integer, or select Choose > Random to enter a random value in the box.
     
     
   • Enter the desired number of Threads. The default value is 2.

4. Press OK to generate the tree.

To control which tree is currently displayed:

There are three methods for choosing which tree is displayed in the Tree view.

• View > Tree commands – Use View > Tree > <Tree name> to make that tree active.

• Explorer panel – The Trees section of the Explorer panel contains a table listing the name of each tree, the method used to create it, and the time the tree was built. To make a particular tree active, click its row in the table. In the example below, three trees are available and their names are: Tree (the default tree), Tree 1 and Tree 2.
  
  

• Tree view tab – The Tree view tab shows the number of available trees as follows: <Number of trees> Tree. The trees themselves are numbered as specified during their creation (see steps above). In the example below, four trees are available, and their names are: Tree (the default tree), Tree 3, Tree 5 and Tree 7.
  
  

To import a Newick-format tree file:

MegAlign Pro can open Newick trees with .newick, .txt or .tree extensions.

1. Make any MegAlign Pro project tab active, or open a new, blank project. Trees cannot be opened from within the Welcome screen

2. Choose File > Add Trees.

3. Select one or more Newick tree files and choose Open. Each tree is added as a named tree in the Tree view tab and the Explorer panel, as described above. The tree name is the same as the file name.

4. (optional) If desired, repeat Step 2 to add additional trees.