Though it may appear to be just a game, Phylo is actually a framework for harnessing computing power to solve the problem of multiple sequence alignments. Citizen scientists play the game by arranging nucleotides. The goal of the game is to maximize the matches and minimize the mismatches between the DNA sequences on the digital game board.

A sequence alignment is a way of arranging the sequences of DNA, RNA or protein to identify regions of similarity. These similarities may be consequences of functional, structural or evolutionary relationships between the sequences. From such an alignment, biologists may infer shared evolutionary origins, identify functionally important sites, and illustrate mutation events. More importantly, biologists can trace the source of certain genetic diseases.

Traditionally, multiple sequence alignment algorithms use computationally complex heuristics—trial-and-error efforts—to align the sequences. This approach requires a lot of computing power given the sheer size of the genome, which consists of roughly three billion base pairs. Humans are good at recognizing patterns and solving visual problems efficiently, so adding citizen scientists to the equation is expected to optimize alignments in ways that the computer algorithm can't.