RadCon allows the user to manipulate a set of source trees.
The commands for manipulating source trees are grouped together in the top half of the Source menu.
The user should note that the commands are implemented on all the trees in a set of source trees whether they are selected or deselected and active or inactive.
Using the commands in the Source menu the user can root, unroot, reroot, reweight and condense a set of source trees. In addition an outgroup leaf can be grafted and leaves can be pruned and regrafted. Furthermore trees from other files can be added to a set of source trees.The Add Trees... Source menu command allows the user to input sets of source trees, from one or more text files, and add them to the set of source trees associated with the active Trees window
The Graft Outgroup Leaf Source menu command adds a new leaf to all the source trees at the root and moves the root onto the newly created terminal branch.
This command is only available if the source trees are rooted.
The Prune/Regraft Leaves Source menu command allows the user to prune and regraft leaves from all the trees in a set of source trees.
This command can cause trees to be inactivated/activated.
The Reroot Trees Source menu command allows the user to specify the terminal branch on which the root is to be placed. The terminal branch is specified by choosing the associated leaf at the tip of the terminal branch.
This command is only available if all the trees in a set of source trees share at least one leaf.
Rooting trees with three leaves will cause them to become active.
All the trees in a set of source trees must be either all rooted or all unrooted.
The Rooting Source menu command allows the user to root or unroot all the trees in a set of source trees.
Unrooting or rooting trees with three leaves will cause them to become inactive or active, respectively.
The Condense Trees Source menu command allows the user to condense identical source trees ,i.e., identify multiple copies of a single tree and delete all but one copy.
In addition, the user can specify the weight of the remaining tree to be the sum, mean, maximum or minimum of the multiple copies (including itself).
The sum option allows the user to reduce the size of a set of source trees without affecting the analysis.
If the set of trees are a set of bootstrap trees the user can specify that only identical trees within the same bootstrap replicate are to be condensed. This function was used in Thorley and Wilkinson (1999).
The Reweight Trees Source menu command allows the user to assign all the trees in a set of source trees the weight of 1 or if the source trees are a set of bootstrap trees to set the weight of each tree to be the inverse of the size of the bootstrap replicate in which it occurs.
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© Copyright 1999, 2000, 2001, Joseph L. Thorley and Mark Wilkinson. All rights reserved.