• The difference between MD5 and SHA256 is that the former takes less time to calculate than later one.
• SHA256 is difficult to handle than MD5 because of its size.
• SHA256 is less secure than MD5
• MD5 result in an output of 128 bits whereas SHA256 result output of 256 bits.

Concluding all points, it will be better to use MDA5 if you want to secure your files otherwise you can use SHA256.