Phylogeny View
The Phylogeny View is used to generate a phylogenetic tree using the sequences in your FASTA file and the TN93 (genetic distance) -based neighbor-joining (NJ) method. Like genetic distance networks, a phylogenetic tree represents the evolutionary relationships among a set of sequences from a group of organisms.
Phylogenetic trees can be rooted or unrooted. Rooted trees provide information about the order of nodes in the tree. The root of the tree is the oldest ancestral lineage of the dataset examined. Unrooted trees show the relationships of the taxa without making assumptions about ancestry. The NJ method used for Phylogeny View infers a rooted tree.
The length of the horizontal branch in a tree is directly proportional to the amount of genetic change in your dataset. The scale bar in the Phylogeny View provides the number of nucleotide substitutions/site in the dataset for the branch lengths in the inferred tree. The vertical lines have no meaning but are used to evenly display the taxa in the tree.
To display the phylogenetic tree, select Phylogenetic Tree from the View menu; the tree opens in a new view tab. You can use the mouse to zoom in and out and use the Center and Scale icon 
to re-orient the tree to its default size and position.
Tree settings can be customized using the Toggle Phylogeny Settings button 
to access the menu. There are three tabs within this menu: Tree, Branches and Leaves.
Modify tree settings using three tabs: Layout, Actions and Meta Layout: Select the Layout tab to change the type of tree, layout, and whether you would like the ruler (scale bar) displayed. You can also stretch the tree vertically or horizontally. This feature is helpful when you have a large tree with many taxa. The stretch feature spreads the branches out and allows for greater clarity. The default is a vertical weighted dendrogram, which is a tree with the branch lengths scaled. The length of the branch is proportional to the number of nucleotide substitutions. A dendogram is a diagram representing a phylogenetic tree that shows how ancestors are related to descendants. A weighted dendogram infers a rooted tree that reflects the structure present in the genetic distance matrix. The figure below shows a horizontal, weighted dendrogram with the scale bar displayed. You can use the horizontal and vertical stretch bars to expand the tree, especially useful for tree with many taxa.
The figure below shows a different layout- a circular weighted dendrogram.
