Trees are input to RadCon as a set of source trees trees and associated with a Trees window.
Trees to be input into RadCon must be stored in either the NEXUS or Phylip formats.
The upper limit on the number of leaves in a set of trees is 500.
The lower limit on the number of leaves in each individual rooted or unrooted tree is 3 or 4, respectively.
Inputting a set of trees with leaves that do not fall within these limits constitutes an input error.
The upper limit on the length of a leaf name is 127 characters.
The lower limit on the length of a leaf name is a single character.
Leaf names which contain special characters or spaces are not permitted unless the leaf name is in single quotes.
Leaf names which exceed the upper limit in length are automatically truncated and a message written to the Log window.
Trees in the same set are not required to have identical sets of leaves as RadCon does not require each tree to contain all and only the predefined leaves.
The NEXUS and Phylip standards are for a set of leaves to be predefined and for each tree to contain all and only these leaves.
In RadCon these standards can be relaxed and missing and undefined leaves permitted in trees.
Trees are not required to have the complete complement of predefined leaves.
If trees contain leaves that are not in the set of predefined leaves this either constitutes an input error or the set of predefined leaves is redefined 'on the fly' to include them.
The adopted protocol for handling undefined leaves can be set using the Preferences command in the Edit menu.
The upper limit on the number of trees in a set is 10,000.
The lower limit on the number of trees in a set is 1.
Once the upper limit is reached any remaining trees are skipped.
The upper limit on the length of a tree name is 127 characters.
The lower limit on the length of a tree name is a single character.
Tree names cannot contain special characters or spaces.
Tree names which exceed the upper limit in length are automatically truncated and a message written to the Log Window.
Trees are not required to have unique names.
Trees in the same set must be either all rooted or all unrooted.
If a set of trees contains a mix of rooted and rooted trees they all rooted or unrooted according to the state of the first tree in the set and a message written to the Log Window.
The upper limit on the weight of a tree is 1,000.
The lower limit on the weight of a tree is 0.001.
If no weight is specified for a tree it is assigned the default weight of 1.
Any specifications of branch lengths are ignored.
A set of trees are treated as bootstrap trees if and only if 1) they have all have a name of the form B_a.b (where a and b are positive integers specifying the bootstrap replicate and the position of the tree within the replicate, respectively), 2) the numbering of replicates and positions is successive and begins with B_1.1 and 3) the trees have identical leaf sets.
The default tree is the tree in the set which is drawn in the associated Trees window. Hence when a set of trees is input if a default tree is specified it appears first in the Trees window and the default tree can then be changed by changing the tree which is drawn in the Trees window
When no default tree is specified the first tree in the set becomes the default tree.
If multiple default trees are specified then the last default tree becomes the default tree.The 10 characters ';,():=[]&*' are special because they provide punctuation in input files.
An input error occurs if an incorrectly formatted file is input or if the values in a correctly formatted file are not within the predefined limits for the program.
When this occurs a dialog box containing a Message indicating the nature of the error is displayed, input is aborted and the offending file is displayed in an Edit Window.
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© Copyright 1999, 2000, 2001, Joseph L. Thorley and Mark Wilkinson. All rights reserved.