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	Phylogenetic Investigator
	Steven Brewer and Robert Hafner (Western Michigan University)
Screen Shots | System Requirements

Phylogenetic Investigator (PI) is a software package designed to facilitate creative problem-solving in phylogenetic analysis for the purpose of teaching and learning phylogenetic inference. Users can identify characters and states, polarize characters, and engage in directed-search phylogenetic tree construction. PI also allows the user to (1) make inferences and represent them one step at a time, (2) vary representational features of their trees (such as angle of divergence and time between speciation events), (3) create reticulate tree patterns, and (4) view all of the character transformations at one time. In addition, PI can generate plausible data stochastically for modeling and practicing tree construction.

PI provides tools for managing and manipulating up to 20 characters of binary phylogenetic data for 15 or fewer taxa. PI has been designed with 2 datasets in mind: the Caminacules and the Dendrogrammaceae (both are included in the Support Materials folder on the Library CD), but other datasets can be adapted for use.

PI uses two windows for data management (Chars & States and Data Matrix) and one for tree construction (Phylogenetic Tree).

The compact version of the Chars & States window is shown on the left. Characters are entered into the top field. Once entered they appear in the scrolling list. States are entered into the lower fields. The three buttons at the bottom allow exchanging character state names (left button), reversing polarity of data in the data matrix (right button), or both (middle button).

The Data Matrix window is shown above. Each row in the matrix represents the data for a taxon and each column represents a character. Characters are coded with symbols for ancestral (0) and derived (1) states. At the upper left is the number of unweighted transitions in the tree. The field at the bottom is user-modifiable and contains the name of the problem.

One possible phylogenetic tree constructed using the data in the Data Matrix is shown above.

System Requirements

Macintosh or Power Macintosh

• System 6.07 or later; System 7.1 or later for Power Macintosh.
• At least 2MB of available RAM, more for complex models.