You may learn to use RAP by testing it. Examples are included in the software, and they can be found in its directory after the installation. They can be loaded and used as follows.
Download the software.
Unpack the software in a new directory:
Unix users: tar xvf rap.tar
Windows users: use WinZip
Compile the software (in an MS Dos session for Windows users)
Launch the software (in an MS Dos session for Windows users)
Load the global species tree by clicking on . Be sure than the filter "species tree file" is selected. Go to the software directory. Load "species.spt". It takes a while because of the tree size and the operations made on it.
The species tree window has changed: it contains new information about the loaded tree: the file name, the leaves number and the root name.
You could launch the editor, in order to see the tree by clicking on . It not necessary for the moment.
Load the included gene trees by clicking on . Be sure than the filter "gene tree file" is selected. Go to the software directory. Load every ".gnt" files. It takes a while too, because a subtree of the global species tree is calculated for each gene tree.
Select each gene tree by clicking on .
Reconcile and root them by clicking on . It takes again a while.
You can see the results by clicking on any . Gene trees are classified with theirs size.
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