Alignment Extraction of a Phylogenetic Data Set

In summary, the following points should be considered when constructing a multiple sequence alignment for a phylogenetic analysis  

The aligmnent step in phylogenetic analysis is one of the most important because it produces the data set on which models of evolution are used. 

It is useful to perform phylogenetic analyses based on a series of slightly modified alignments to determine how ambiguous regions in the aligmnent affect the results and what aspects of the results one may have more or less confidence in. 

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