PolyMFind is a program that scans through a multiple genome alignment to identify and classify all polymorphisms. The multiple sequence alignments are generated by Mauve. Since the alignment is generated using sequences stored in CoGe, PolyMFind can query the location of each polymorphism and identify any underlying genomic feature. If the genomic feature is a protein coding gene, the change in coding sequence is assessed to determine if it causes a frameshift, synonymous, or nonsynonymous mutation.
Note: There a several sources of errors for these polymorphisms that from three major factors: