Module 8: Phylogenetic Analysis

 

Tree of Life Project and Tree-Building Software

Cladistic Methods module 8 contents Exercise 8 back to the index of modules


  • Tree of Life: This University of Arizona site coordinated and edited by David Maddison is an excellent, whole-world distributed, Internet project containing information about phylogeny and biodiversity of organisms on Earth, their history, and characteristics. All the information is linked together in the form of the evolutionary tree that connects all organisms to each other.

    The images in this integrated web site show an amazingly wide variety of organisms from all corners of the world, living in a wide range of environments. The links show varying nutritional requirements and reproductive behaviors. This is the Tree of Life Project Root Page which shows the relationships of the major lineages of living things. (A Page on Terrestrial Vertebrates with Digits) is an example page showing images and a small region of the whole tree.

  • Software for building phylogenetic trees: There is a wide variety of software available free of charge, at a minimal charge and at very expensive prices.

    • PHYLIP (Phylogeny Inference Package) is a comprehensive package of applications that include parsimony, distance matrix, and likelihood methods. Data types that can be handled in the package include molecular sequences, gene frequencies, restriction sites, and distance matrices. This package can be downloaded for free.

    • GCG (Genetics Computer Group) The GCD package is a widely used commercial software package with algorithms for analyzing different evolutionary relationships. (It is expensive to license it, though!)

    • An exhaustive compilation of various phylogeny software can be found at this University of Washington site. The different software are annotated well and grouped by the available phylogenetic methods they contain and by the computer systems that they work on.


Cladistic Methods module 8 contents Exercise 8 back to the index of modules

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