For the most part, the protocols that run on top of IPv4 run unchanged on IPv6 as well. TCP and UDP are their old selves, as is almost everything that uses them. The notable exceptions are those protocols that transport IPv4 addresses internally. FTP is one such protocol, and has extensions to support IPv6, ditto NTP. The IPv6 version of ICMP, ICMPv6, is not much different from ICMP.
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The title of this document is:
Higher-level protocols
URL:
http://www-uxsup.csx.cam.ac.uk/courses/moved.ipv6_basics/x141.html