To generate a new phylogenetic tree:

  1. Add sequences and perform a multiple alignment.
  1. Use any of the following methods to direct MegAlign Pro to create a tree using the algorithm you specify. For helpful advice on choosing the best tree for your data, see this December 2020 DNASTAR blog post by Brian Walsh, PhD.

    • Click on the Tree tab to open the Tree view. Choose one of the two available 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.

      • Maximum likelihood: RAxML was developed by Stamatakis (2014). Comprehensive information about options associated with this algorithm can be found in the RAxML Manual (PDF).

    • In the Trees section of the Explorer panel, press the green plus-sign tool () to the right of the table. In the Using drop-down menu, select the desired algorithm.

    • Use the menu commands Tree > Compute Phylogeny Using > Neighbor Joining:BIONJ or Tree > Compute Phylogeny Using > Maximum Likelihood: RAxML.
  1. Customize settings based on the algorithm you chose.

    • If you chose Neighbor joining: BIONJ:



      • Type in a new Name for the tree or keep the default name of Tree <number>.

      • If you change your mind and want to use the other algorithm, choose it from the Using drop-down menu.

      • Press OK to generate the tree.

    • If you chose Maximum Likelihood: RAxML:



      • Type in a new Name for the tree or keep the default name of Tree <number>.

      • If you change your mind and want to use the other algorithm, choose it from the Using drop-down menu.

      • To add a bootstrapping step to the calculation, place a checkmark next to Bootstrap analysis; if you do so, another option appears. 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.

      • Press OK to generate the tree.
  1. (optional) Use the Style panel’s Tree section to customize the tree as desired.
  1. (optional) Create another phylogenetic tree using a different algorithm or different settings for the same algorithm. See Work with multiple trees.

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