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The first known game to have developed a coordinated speedrunning fanbase was DOOM, with several websites collecting demos (files with recorded playing) around 1994.
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An essential part of speedrunning is to find the shortest feasible route through the game. In highly non-linearly structured games, which are almost exclusively preferred for speedrunning purposes, there is often no obvious choice. The shortest possible route might contain so many obstacles that it is virtually impossible to use, and it is therefore often necessary to find a compromise between ease and distance. Depending on how the player's skill improves, faster but increasingly difficult routes may be chosen.
The best routes do in fact rarely rely upon the paths and progressions that were designated by the developers. Skilled players will usually discover ways to finish parts of the game in a different order than was intended, and they consequentially often find ways to skip parts of a game entirely. Using these shortcuts is sometimes called sequence breaking. Shortcuts are often possible because their existence has been overlooked by the developers, but they are sometimes actually implemented intentionally.
Sometimes a glitch will allow for an interesting speedrunning opportunity. The classic example is being able to walk through a wall due to an inferior game engine. Whether taking advantage of such an opportunity results in a legitimate speedrun is a matter of debate.
There are two big subgenres of speedruns: Unassisted speedruns and tool-assisted speedruns (sometimes referred to as "time attacks"). Unassisted speedruns are done in real time using only whatever features there were in the actual game, while tool-assisted speedruns also use the features found outside the game, such as the "save-state" feature found in emulators.
Unassisted speedruns are usually considered more impressive, since they require the most skill, planning, and practice to pull off. Official recordkeeping only considers unassisted speedruns. Some believe this is the only real way to do a speedrun, even going so far as to describe tool-assisted speedruns as "fake" or "cheating."
The tool-assisted speedruns try to avoid comparisons to the unassisted runs, as this would be unfair to the players. In unassisted runs, it would be unacceptable to use emulator's save-state features to take a shorter but more dangerous path, saving the game when passing an obstacle. Likewise, many unassisted speedrunners frown upon glitch abuse, while it is highly desirable in the tool-assisted community.
Tool-assisted speedruns are not done to show off one's playing skills, but more to show off all kinds of crazy things that are theoretically possible in the game but impossible to do in practice. While speed is desired, the focus is on entertainment. For example, there is a famous tool-assisted speedrun of Super Mario Bros. 3 by "Morimoto" that finishes the game in approximately 11 minutes - the fun is in the breathtaking speed and overall craziness of the game, not the skills. The video has since been "obsoleted" by a faster tool-assisted speedrun, but this video is still the best-known example of its kind.
The controversy revolves around the similarity between the finished products. Websites exist dedicated to each side in the hopes that the movies will be considered separate. However, some individuals have allegedly tried to submit tool-assisted speedruns as unassisted speedruns. Without careful analysis, it is hard to tell the difference between the two, and this undermines the effort put into unassisted speedruns.