To gain a Phylogenetic overview of an alignment, select Alignment | Phylogenetic Overview from the menu bar. This brings up the Phylogenetic Overview dialog.
This dialog allows you to view a Jukes Cantor/Neighbor Joining tree for every window position within the alignment (based on the window settings you specified). VCR-like playback controls are also provided to run an animation that displays every tree automatically.
The number of trees that can be drawn is based on the number of windows that are available. By adjusting the current window size using the Window size control you can specify how many windows the alignment will be partitioned into.
Modifying either of these values will adjust the slider control under the tree window, allowing it to select (for display) more or less windows. The Window position label under the slider gives the current window position, along with the nucleotide starting and ending values for that window.
You can also animate the tree, and watch how it changes as the window moves over the alignment. To accomplish this, first select a suitable window and step size, then decide upon the delay time (in milliseconds) that each tree will be visible for. You can then use the animation buttons to control playback.
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Rewind - return the animation to the beginning (moving the window back to its initial position) |
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Step Back One Window - move the window back one (step size) increment |
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Stop - stop the animation that is currently playing |
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Play - start (or restart) the animation from the current window position |
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Step Forward One Window - move the window forward one (step size) increment |