7.1 years ago by
From this and this I would say the scale bar probably indicates number of amino acid changes per site (that's what it showed in those two papers). However, from the manual it seems that the bar can be either show distance or time scale. To quote:
Show Distance Scale. This allows you to show or hide the scale bar
distance, to enter the unit used and to choose its length and the interval between tick marks.
Show Time Scale: This presents the option of showing or hiding the divergence time in the
scale bar, and to enter the units used. You also can determine the interval between two major
ticks and two minor ticks. To activate this option the divergence time for a node or the
evolutionary rate must be given.
If you can show a picture of what your phylogenetic tree looks like, or at least give some numbers it is showing, it is easier to infer what the bar shows.