The Trees section of the Explorer panel is used to control which phylogenetic tree is displayed in the Tree view, and allows you to create additional trees or delete them.

To open the Trees section, click on the Explorer tab (); if the Trees section is closed, expand it by clicking the Trees bar. Alternatively, choose View > Explorer > Explorer or View > Reset Panel Layout.

Prior to performing a multiple alignment, the Trees section is empty. Once an alignment has taken place, the Trees section contains a table with one row for each phylogenetic tree that has been generated. The table contains three columns:

  • Name – The default tree generated during multiple alignment is always named Tree. Other trees are assigned names during the use of the Tree > Compute Phylogeny command.
  • Method – The algorithm used to create the tree. The default tree is always created using Neighbor joining: BIONJ, which is abbreviated to BIONJ. Other trees may use that method or the Maximum likelihood: RAxML method, which is abbreviated as RAxML.
  • Status/Completion – Time the tree took to complete.

To the right of the table are two tools:

Icon Name Purpose
Computes a new phylogeny for the aligned sequences To create a new tree and add it to the table. This is a shortcut to the Tree > Compute Phylogeny command. See the topic Phylogenetic Trees for instructions on adding a tree.
Remove phylogeny To delete a selected tree from the list.

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