Omega-3 is a broad class of unsaturated fatty acids that is found in both salmon and flax oil. The main essential fatty acid that these oils provide is alpha linolenic acid (ALA). Salmon oil has the added benefit of also providing EPA (eicosapentaenoic acid) and DHA (docosahexaenoic acid). Flax oil does not provide them, but a healthy liver will convert the ALA from flax oil into DHA and EPA. The reason salmon oil already has these two fatty acids is that the livers of the fish have converted the ALA that they ate from plants into DHA and EPA. For anyone with impaired liver function, salmon oil is probably the better source.
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