>>Thanks to all for the references. I'll have to get my hands on the various papers when I have a chance. But something required to really evaluate the results is an understanding of the statistical analysis of the data. Typically this seems to consist of the use of a software package. Is this software readily available and is it expensive?



It's not so much a matter of statistics as simply generating the tree, which is very memory consuming.



The software for that is widely available. Some is free (e.g., MEGA from www.megasoftware.net, primarily for distance analyses and Neighbour-Joining approaches; MrBayes for Bayesian analysis; Phylip for a whole bunch of things), some is available for more or less reasonable prices (PAUP* is probably the industry standard for many types of analysis).



Joe Felsenstein has a great page with links to all the different programs that are currently available (link below). The problemw itha lot of them is that (i) you need to know what you want to do before you start using them, and (ii) the documentation that comes with many is pretty sketchy, so learning to use them by yourself is pretty time-consuming and frustrating. The first thing you really need to do is to pick up a book on phylogenetics (most evolution and even general biology textbooks will have a chapter on the basics) and molecular phylogenies ot get a general grasp of the basic underying ideas.



Cheers,



Wolfgang
Joe Felsenstein's Phylogeny Programs Page


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