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Chapter 7 Web Search Terms

Internet addresses of the major sources of phylogenetic analysis programs are given throughout the text and below. Using search terms on the Web such as phylogenetic analysis, the individual methods of phylogenetic analysis (search for maximum parsimony, distance methods, or maximum likelihood AND phylogenetic), or those listed in Table 7.1 should lead to the current Internet sites. Additional search terms are given below.

EMBOSS Programs and programming modules for phylogenetic analysis like those of PHYLIP.
MrBayes Phylogenetic analysis using Bayesian estimates of most likely trees.
PAUP Phylogenetic analysis using parsimony; however, version 4 includes maximum parsimony, distance, and maximum likelihood methods.
PHYLIP Phylogenetic inference package; a collection of programs for phylogenetic analysis using maximum parsimony, distance, or maximum likelihood methods.
PAML Programs for phylogenetic analysis by the maximum likelihood method.
TREE PUZZLE Phylogenetic analysis by the maximum likelihood method.


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