For most of my life, we have thought of snakes as being closely related to lizards. Both snakes and lizards are squamates (the order Squamata), but all my childhood reptile books placed snakes as being part of a distinct suborder called Serpentes.
However, taxonomy has moved onto a cladistic model, where we group organisms based upon their common ancestry. A clade is defined as including all descendants of a common ancestor, and keeping snakes a specially defined entity distinct from lizards is problematic.
A recently published paper on the Komodo dragon genome reveals why this is a problem for a cladistic classification model. The authors compared the genomes of komodo dragons with the Burmese python, several species of lizard and lots of other tetrapods.
A phylogenetic tree was drawn from the comparisons.
The Burmese python does not fit outside of the “lizard” clade. It fits within that clade, and if we are to use cladistic classification, then we must place snakes within lizards.
Snakes are a particularly specialized form of lizard, and as it should be noted, they are not the only legless lizards known. There are glass lizards and worm lizards (some of which are not entirely legless) that have a similar sort of body design to the snakes.
Snakes are the most wildly distributed legless lizards, but we probably should recognize them as lizards and not some sort of special grouping distinct from lizards.