Phylogenetic Analysis with PHYLIP

TABLE 18.4 Some software programs for phylogenetic analysis of biosequences 

COMPONENT CT http //taxonomy.zoology.gla.ac.uk/rod/cplite/guide.htm 

DAMBE G DC, DM, ML, P http //aixl.uottaw.ca/ xxia/software/software.htm 

EDIBLE ML http //ebi.ac.uk/goldman/info/edible.html 

GDA DM http //hydrodictyon.eeb.uconn.edu/people/plewis/softwaie.php 

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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. 

The home page of WebPhylip consists of three windows. The left window is the command window for selecting and issuing the execution (Run) of the analysis/ operation. The analysis results appear in the upper window. The lower window is the query window with options, a query box for pasting the query sequences (in Phylip format), and Submit/Clear buttons. To perform phylogenetic analysis, select DNA/Protein for Phylogeny method in the left window to open the available analytical methods (parsimony, parsimony + branch bound, compatibility, maximum likelihood, and maximum likelihood with molecular clock for DNA whereas only parsimony for protein). Click Run (under the desired method) to open the query window with options. Select the appropriate Input type (either interleaved or sequential), paste the query sequences and click the Submit button. The analytical results are displayed in the upper window (Figure 13.4). 

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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