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What kind of synth is used to get a sound like this flute: http://www.youtube.com/watch?v=MC6aAs4kkbY
I saw Jon Brion use one live and he got that sound out of a small synth, but I'm wondering if the sound can be achieved through a VST, or if i could make it myself in Ableton.

Orchestra

sounds like a mellotron to me. that guy was prolly triggering some mello samples using that little keyboard. i mean he obviously didn't use a real mellotron coz those are rather big, basically an old ass kind of sampler that uses tapes for each sampled note.

anyway, have your pick below.

VST
Redtron 400 by Artifake Labs
Tapeworm by Tweakbench
Nanotron by Dream Vortex Studio
Stringer by FalkeLab
Tapeotronic, part of the amazing Elektrostudio pack

SAMPLES
The Taijiguy Mellotron by Real Music Media - you will need the free sfz plugin to play with these. worth getting.
Mellotron Samples by leisureland.us - no mappings for these AFAIK

there you go, all freeware. and if you really wanna pay, the only one worth it is this maybe:
M-Tron Pro by GForce Software

but, as usual, with all the freebies around, why pay the big bucks?

sounds like a mellotron to me

yep definitely has that mellotron sound

M-Audio M-tron Pro (the biggest mellotron simulation, costs moneeey...)

Tapeworm (free! http://www.tweakbench.com/plugins/tb_tapeworm_2_0.zip)

Nanotron (free! http://www.dream.vortex.btinternet.co.uk/nanotron2.zip)

Meltron (free! http://www.mediafire.com/?cw3smm9zgyd)

Also, If you own Absynth 3, there are some kick ass presets simulating flute (presets called Negative flute, "something" flute, snakewind or something like that)