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I recommend the "Apophysis Bible" written by the amazing ~TaraRoys for beginning users to get started.
Thank you very much =TyrantWave for allowing me to use your "heart" plugin in the old variation pack as well as your base form pack for the default templates!
Plugins go to <Apophysis directory>\Plugins and templates to <Apophysis directory>\Templates
Use the T500-version only if you got plenty of system memory (>= 4GB) - it allows up to 500 transforms per flame which will blow up your RAM if you got a weak box.

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It got thumbnails
It got missing plugin detection
It got flame templates
It can handle 3D flames because it's based on *Zueuks 3D-hack
It is able to store metadata into rendered JPEGs such as title, author and parameters
It has an easy-to-use-and-extend template system to get you started fast
It got a revamped user interface to allow it integrate into the beautiful modern windows shells
It got numerous smaller enhancements such as hiding unused variations and variables as well as naming transforms
It can save your work automatically in given intervals
It can show you whether your render will exceed your memory boundaries
It takes advantage of all the Windows 7 shell goodies like jumplists and taskbar progress view

... and so much more!

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But what if you dont have Windows 7?
No problem! You can also run it on Windows XP and Vista of course - allthought in-taskbar progress display, jump lists and thumbnail toolbar will not be available.

How to install it?
It cant be easier. Just download the original Apophysis 2.02 and use the installer. After that, copy the file Apophysis7X-*****.exe (***** = "normal" or "T500") in the install folder and launch it with that file. You can also pin the file onto your Windows 7 taskbar, if you want.

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Apophysis V2.08.7X
Copyright ©2001-2004 Mark Townsend
Copyright ©2004-2008 Peter "zueuk" Sbodnov, Piotr "utak3r" Borys
Copyright ©2009-2010 Georg "xyrus" Kiehne