Programs: Phylogenetic Independence


Phylogenetic Independence (PI) is a program written by Jeff Reeve and Ehab Abouheif to conduct the Test For Serial Independence (TFSI) on continuously valued characters and the Runs Test on discretely valued characters (Abouheif 1999). The TFSI and Runs Test are used to test the assumption of phylogenetic independence within a set of comparative data, i.e., to test whether a trait is significantly associated with its phylogenetic history. This version of the program can perform the TFSI and Runs Test using either fully resolved phylogenetic trees or an unresolved trees (i.e. one with polytomies). Please see: Abouheif, E (1999) A method to test the assumption of phylogenetic independence in comparative data. Evolutionary Ecology Research 1: 895-909 for a detailed explanation and for information regarding the TFSI and Runs Test.

The following article statiscally validates the test for serial independence.
"Testing for phylogenetic signal in phenotypic traits: New matrices of phylogenetic proximities" (2008) Sandrine Pavoine, Sebastien Ollierb, Dominique Pontiera, Daniel Chessela, Theoretical Population Biology 73: 79-9.


Download The Windows PC version Phylogenetic Independence version 2.0
(This program package includes the program, instructions, and an example file. It is provided as a Zipped folder)

Download The command line version compiled under Red Hat Linux Phylogenetic Independence version 2.0
(This program package includes the program, instructions, and an example file. It is provided as a Zipped folder.)

Download R package - Information for test