Synfig Studio has incorporated recently the control of video codec and bitrate for ffmpeg renderer. If you install the latest version from our website you'll get benefit of that feature. With it you could export directly to a video file format without need to assemble the png sequence in any external application. Use ffmpeg as target renderer and .avi or .mp4 as extension and the proper codec and video bitrate at the renderer parameters dialog. Check out the release notes: http://www.synfig.org/en/news/releases/89-release-06201
If you want to use the old style, I recommend to use Avidemux. It nicely imports the png sequence and produce fine video outputs. Be sure to set the frames per second at avidemux to match your animation frame rate, because it cannot deduce it from the png sequence. Avidemux is opensource and available in the main platforms.
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