Alignment Building the Data Model

Phylogenetic sequence data usually consist of multiple sequence alignments the individual, aligned-base positions are commonly referred to as sites. These sites are equivalent to characters in theoretical phylogenetic discussions, and the actual base (or gap) occupying a site is the character state.  

A typical alignment procedure involves the application of a program such as CLUSTAL W, followed by manual alignment editing and submission to a treebuilding program. This procedure should be performed with the following questions and considerations in mind  

Which Alignment Procedure is Best for Phylogenetic Analysis The short answer is the method that is closest to understanding the evolutionary relationships 

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