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You can always reconvert with another video editing/conversion program afterwards if the video editing/3d software you currently use does not have export options for mkv etc. I believe there are links on the video conversion wiki page for free video converters that have mkv support.
Tools you need
- video encoder: we recommed ffmpeg because it can read many formats and convert it with excellent quality.
- subtitle editor for the format: Advanced Substation Alpha (ASS) / encoded File Encoding = UTF8
- mkv editor like MKVToolNix