Alignment

Sixth Step:

The sixth step in the molecular process is alignment, following these techniques:

• Sequences (for each sample) that are clean and have been appropriately verified may be added into an alignment program (such as Mesquite) that allows homologous regions to be matched up, such that non-homologous regions can be evaluated and ambiguous/poorly aligned regions may have to be removed
• The alignment can also be used for primer design – areas of homology between taxa of interest, in an area of the gene of interest, may be good candidate primer regions