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POP and IMAP are the two most common protocols used for accessing email. Both have their pros and cons; the following brief descriptions will help you decide which is best for your usage patterns. For more detailed descriptions, see the links to the wikipedia articles at the bottom.
POP (Post Office Protocol) will download messages from the email server to the email client on your personal computer. Afterwards your email client can be set to immediately erase the newly downloaded messages from the server, to leave them on the server for a specified length of time, or to delete them from the server when they are deleted from the email client. POP is most useful when the mailbox is only being used on one computer. Since email can be removed from the server when no longer needed, more of your allotted server space is available to hold new incoming messages.
IMAP (Internet Message Access Protocol) accesses all mail on the server and downloads them for viewing when needed. Status of the message (read/unread) is tracked on the server. If more than one computer accesses the same mailbox, all messages stored on the server will be available and status will always be synchronized between them. IMAP consumes more of your allotted server space since all messages are stored there, but is much more convenient for users of multiple personal computers.
For more information see these articles:
http://en.wikipedia.org/wiki/Post_Office_Protocol
http://en.wikipedia.org/wiki/Internet_Message_Access_Protocol
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