The Phylip format is a format for storing phylogenetic information, including trees, morphological characters and nucleotide sequences.
RadCon can input trees stored in the Phylip format.
The Phylip (PHYLogenetic Inference Package) format is described by Felsenstein (1993) who developed it for use by programs in his Phylip package. The package which includes the programs, C source code and documentation can be downloaded free from http://evolution.genetics.washington.edu/phylip.html.
A Phylip tree file consists of a series of tree descriptions.
An example Phylip tree file
This Phylip tree file contains two trees. The first tree has four leaves i.e. Fulmarus_glacialis, Calonectris_diomedea, Puffinus_puffinus and Puffinus_yelkouan. The other tree contain all and only these leaves but differs in the cladistic relationships it posits among them. The trees are both rooted, and have a weight of 1. The trees have the names tree1 and tree2, respectively.
The Phylip standard is for the number of leaves and the name of each leaf to be predefined in the first tree description and if subsequent trees do not contain all and only these leaves this is considered an input error.
In RadCon this standard can be relaxed and missing or undefined leaves permitted in subsequent trees.
RadCon does not require subsequent trees to have the complete complement of predefined leaves.
This allows trees with non-identical leaf sets to be input and allows the production of supertrees.
If trees have leaves that were not predefined RadCon either 1) treats this as an input error or 2) redefines the leaf set 'on the fly' to include them.
The adopted protocol for handling undefined leaves can be set using the Preferences option in the Edit menu.
Allowing the leaf set to be redefined 'on the fly' facilitates the production of supertrees as it allows tree descriptions from different files to be pasted into a single Phylip file.
Tree descriptions describe the structure of trees.
The Phylip format adopts the Newick format for storing tree descriptions.
RadCon is currently unable to read tree names from Phylip format files. Trees are assigned the names tree1, tree2 etc according to their order of occurrence in the file.
Trees input to RadCon using the Phylip format are all input as rooted.
RadCon is currently unable to read tree weights from Phylip format files. Trees are assigned the default weight of 1.
No provision is made in the Phylip format for the designation of a default tree.
The first tree in a Phylip format file is designated the default tree and is the first tree viewed in the Tree Window.
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