PHYLIP software

Notes 1. Taken from Phylogeny Programs (http //evolution.genetics.washington.edu/phylip/software.html) for PC-Windows. 

Phylogenetic analysis is the means of inferring or estimating evolutionary relationships. Nucleotide sequences of DNA or RNA and amino acid sequences of proteins are the most popular data used to construct phylogenetic trees. Methods of phylogenetic analysis using sequence data are introduced and performed with a software package, PHYLIP locally and online. 

Phylip (Phylogenetic Inference Package) is a software package comprising about 30 command-line programs that cover almost any aspect of phylogenetic analysis... 

A discussion of the interpretation of enzyme activity banding patterns and the analysis of electrophoretic data is beyond the scope of this chapter. Details on the interpretation of zymograms can be found in several of the references cited herein.10 11 22 Richardson et a/.10 provide a thorough discussion of data analysis and present several detailed examples of analyses taken from the literature. Among the major computer software packages currently available for data analysis are BIOSYS-1 23 PAUP,24 PHYLIP,25... 

PHYLIP and PAUP compete as the most widely used phylogenetic analysis software, although other newer applications such as PUZZLE are begiiming to compete. Here, PHYLIP and PAUP will be described in the most detail, with references made to other available packages that have useful features. However, the number of programs available is now so numerous, many each having their own useful features, that the... 

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