I am trying to analyze census files but I find it confusing to define regions of tracts or zipcodes. I noticed that the postal ZipCodes are messy as there are some overlapping {some zipcode regions are within others, as an example in new york there are some empires as zipcodes}.

A quick look on http://geocommons.com/search.html I could find a lot of options, but couldn't decide. What I found:

As an example, In this link I found two files.

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zctas are defined by the census bureau for each decennial census, zip codes are defined by the us postal service detail here .. they do not change from one survey to another. the census bureau does continually update boundaries, which is why you see two cartographic boundary files in your link. search for the word change inside http://www2.census.gov/geo/pdfs/maps-data/data/tiger/tgrshp2014/TGRSHP2014_TechDoc.pdf for more detail about that. it's unlikely to affect new york city

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