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Gabriel
It would be a little strange for CT to not have any tonality estimation in its commercial encoder.
Hmm I wouldn't be that surprised - I think Dolby's AAC encoder described in their AES paper didn't use tonality esitmation as well, and I know for a fact that couple of other commercial LC-AAC encoders do not use tonality estimation

I cannot reveal names, of course

Not having a tonality estimation might not be so problematic especially at the very low bit rate CBR - where maintaining stable NMR and avoiding spectral holes is much more important than avoiding artifacts of a problematic harmonic structures (hello pitchpipe) - and for high bitrates, you could overcode anyway (like Dolby is doing in A52 specification, or as described in fast AAC AES paper).
Also, 3GPP reference code obviously misses some things from what I saw, for example TNS encoding, uses fixed multiplication of the post-TNS thresholds (factor 0.25), while in the specs it is clearly called "a table" - and, well, some more.
Also - quality difference clips between CT (commercial) and 3GPP - just try Waiting.wav @48 kbps, 48 khz with CT encoder and 3GPP reference source (I am talking about HE-AAC , not v2 with PS) - and check the amount of stereo reduction (which is being done to improve the LC SNR on the expense of stereo image) - while 3GPP code almost completely downmixes LC part to mono - CT maintains better spatial image (not perfect, though, but much better) - which means it had more SNR available so it didn't need to reduce stereo image that much (or the 3GPP reference code algo is broken).
There are many more - i.e. with castanets.wav you can clearly hear typical short block distortions @48 kbps (HE, too) at the end of the "fast" castanets clip - while they are not there with CT's commercial encoder, etc.. etc...
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Most importantly, I'd like to know if one will have to install the whole new Nero 7 just to use the improved AAC+ for which Ivan Dimkovic has been providing drumrolls. ( I'm darkly suspicious of any software that's compatible with Blu-Ray.)
Unfortunately, I cannot tell you that. What is sure, at the moment, the new encoder will be available with N7
web release - and about its future and possible other applications, no more public info is available at this moment.
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ckjnigel
I also am wondering how the proprietary elements that Coding Technologies and Ahead put into their encoder applications will affect willingness of hardware manufacturers to create portable devices that can play the files.
You can be pretty sure that HE-AAC encoders (at least for Nero I can be 101% sure, and for CT I have no reason to doubt it is also the case) do not put anything proprietary in the elementary bitstream - which is what it is needed to be decoded by the ISO decoders ;-) There are proprietary algorithms, of course - but all of them produce standard compatible MPEG-4 streams.