If you are using a Linux distribution which manages sound using PulseAudio, you can still use amixer to change the master volume or to mute/unmute your speakers via command line.

As an example, to decrease the master volume by 5%, run:

amixer -D pulse sset Master 5%-

Similarly, to increase the master volume by 5%, run:

amixer -D pulse sset Master 5%+

To mute your speakers, run (you may also use unmute):

amixer -D pulse sset Master mute

Finally, you may toggle the "muted" state of your speakers with this command:

amixer -D pulse sset Master toggle