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:
|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.|
Need more help with this?