MASED can produce trees from a multiple alignment. DNAMAN calculates the homology matrix and establishes related distances between all pairs of sequences. When you press the Output button, a popup menu appears. You may choose a distance matrix of the alignment, a phylogenetic tree or homology tree.
Distance matrix. This matrix shows related distances between all pairs of sequences in the alignment. The low value presents a low divergence (high homology) between two sequences. The maximum distance is 1.0, which indicates no homology between the two sequences.
Homology tree. This tree is setup with the distance matrix using the UPGMA method (Sneath and Sokal, 1973, Numerical Taxomomy, San Francisco, USA)
Phylogenetic tree. This tree is setup with the distance matrix using the Neighbor-Joining method (Saitou and Nei, 1987, Mol. Biol. Ecol. 4:406-425)
Bootstrapping of a phylogenetic tree. You may carry out a bootstrapping test for the confidence value of the phylogenetic tree.
Homology tree is drawn in a graphic window. It shows related homologies between two sequences or groups.
The sequence names are listed at the left of the graph. Sequences with high homology are grouped together. A rule of homology level is placed on top of the graph. You may adjust the position and size of the trees in the graph.
-Move tree. Place the cursor on the rule. By pressing and holding the left button of the mouse, you may move the tree on the screen.
-Change shape and size.
There is an option to display or hide homology number on the branches. By clicking the %On/Off button, you may switch the option.
Phylogenetic tree shows related homologies between any two sequences in a multiple alignment. When you choose the Output Phylogenetic Tree menu, a dialog box appears to ask for a bootstrapping test number. If you enter a number less than 10, the test will be omitted. Otherwise, DNAMAN performs the test with the entered number. Bootstrapping is a threaded process in DNAMAN. Therefore, you may perform other analysis functions during bootstrapping.
Two windows are opened when the tree is constructed: a Text window containing the description of the tree and a Graphic window showing the graphic view of the tree.
The tree is described using variations of "Newick 8:45" format adopted by the NEXUS format and by PHYLIP. The description starts at root and follows the visit of all nodes. If the node is a leaf, the leaf is recorded and then return to its immediate ancestor. If the branch leading to the leaf has a length, the length is recorded immediately after the leaf with a colon, e.g. "Mouse:0.025". There are three indicators if the node is not a leaf. 1) A left parenthesis "(" indicates the first visit and the next node is the leftmost. 2) A comma "," separates the descendants of the same ancestor. 3) A right parenthesis ")" shows all descendants of the same ancestors have been visited. A node label (e.g. a bootstrap value) may be indicated immediately after the ")" (e.g. ")99"). If the branch leading to the node has a length, the length is recorded immediately after the leaf with a colon, e.g. "):0.025". A semi colon ";" indicates the termination of description.
Phylogenetic tree is drawn in a graphic window. There are six check boxes on top of the graph: Unrooted Tree, Radial Tree, Rooted Tree, Branch Length, Seq Weight and Bootstrapping. If the status of any check box changes, DNAMAN will redraw the tree according to the change.
-Move tree. Place the cursor on the scale. By pressing and holding the left button of the mouse, you may move the tree on the screen.
-Change shape and size.
Place the cursor on the most left vertical line from the root of the tree, or on the last horizontal branch (bottom) of the tree. When the cursor switches to an arrow, press and hold the left button of the mouse to change the shape and size of the tree.
You may change the display options of phylogenetic tree by using the Edit | Options command. This command opens an Options dialog box. You may change all options described above, move or resize the graph and change text fonts used in the graph.