Ya estás allí
means
You are already there
But:
¿Ya estás allí?
means
Are you there yet?
Another example:
It would be wrong to say 'Ya no' when trying to mean 'Not yet'. The translation of 'Not yet' is 'Todavia no'.
However, 'Ya no' is a very popular phrase used to say 'Not anymore'.
So the word 'Ya' means sometimes 'yet', sometimes 'already', and sometimes 'anymore'?