There are three basic guitar construction techniques (with several variations on each). All three construction/design techniques have merit and have attracted ardent followers. I personally prefer the Neck-Through/String-Through-Body construction employed in the Anarchist because of its total commitment to tone.
Neck-Through-Body construction is virtually indestructible: it means that the neck extends all the way through the guitar instead of being either bolted on (Bolt-On) or glued into (Set-Neck) the body.
The "body" of the guitar is actually comprised of "wings" that are attached to either side of the Neck-Through section of wood. This guitar construction method provides the least resistance to the vibrations produced when the instrument is played, resulting in a rich, thick tone and extended sustain.
You will likely spend more for a neck-through-body guitar because they are more expensive to build. Examples of neck-through-body guitars are the high-end Jacksons like the Solist, Ed Roman's Abstract Guitars, and Ibanez makes a nice X series neck-through model.
Set-Neck design is very common. Gibson Les Paul and PRS are examples of Set-Neck guitars. In this construction method the neck is glued into the body pocket (the deeper into the body the better). This layer of glue can present a barrier to tone transference from the body. On better guitars, wood glue is used in the pocket that absorbs into the wood of the neck and body rather than hardening into a mass that creates a solid barrier to sound.
Bolt-On design is as the name suggests: the neck is bolted onto, or in cases of the better constructed guitars, into, the body of the guitar. Many love the Bolt-On method of construction because of the freedom it allows for adjusting and even swapping necks. Fender Stratocaster is an example of a bolt-on guitar, The use of bolts or screws to secure the neck is said to have a tonal advantage over the Set-Neck because no glue is used, thereby allowing total wood to wood contact between the neck and body for better tone transference.
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