mkv tool

mkvtoolnix package includes all main mkv tools: mkvmerge, mkvextract, and mkvinfo. For example, merge two avi files into a mkv with subtitle files (idx and sub):

$ mkvmerge --append-to 2:0:0:0,2:1:0:1 -o dvd.mkv dvd1.avi dvd1.idx +dvd2.avi dvd2.idx

'2:0:0:0(format is: source_file_id:source_track_id:destination_file_id:destination_track_id)' specifies that the track 0 of source file 2 (i.e. dvd2.avi) is appended to the track 0 of destination file (i.e. dvd1.avi), and user may try this command without append-to option firstly, as may result in merging failure error. It's unnecessary to specify the sub file here.