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Installation of SKSE64 is very simple, you basically need to copy and paste a few files. Look for the line labled Current SE build 2.0.19, and click on the underlined link 7z archive to begin the download. The remainder of this guide is geared towards ModOrganizer 2 users and is still perfectly valid. I believe the newest version autodetects SKSE64 and installs it correctly for you. The mod will then install correctly with no additional steps required. If you install the SKSE64 download with Vortex, simply change the input type to Dinput. One of which is the input type designation. It happens to be a very well designed and stable manager with a lot of features not found on other mangers.
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* Note - Since this guide was released Vortex has replaced NMM as the new standardized modding tool offered by Nexus mods. * I will provide basic installation instructions, along with a slightly more advanced method that will make installing future updates or removing the files all together much simpler. SKSE can not be installed with a manager, the files must be extracted and copied manually. The only tool required for SKSE64 installation is the downloaded archive.
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