Software for syncing and muxing audio track with video track?

[uranometria]

I'd appreciate recommendations for programs capable of syncing and muxing audio/video tracks.
It would also help to have audiograph shown.
If the program also works with subtitles, it'll be wonderful.
By the way, I'm working with mkv container, H264 10bit/8bit, FLAC, AAC, and AC3.

Thank you.

[Baldrick]

I would try some advanced video editor like sony vegas, moviestudio pro, aviutl(free). But most wont support mkvs directly though...maybe if you remux the mkv to mp4 with mkvtomp4 first.