APE (R) package NJ tree - what's the scale?

Question

[biogirl]

Hi there, another APE related question!

I have built a tree using the 'dist.gene' function of APE in R, to calculate the pairwise distances of my input data, and then constructed a neighbour-joining tree. I then noticed the scale bar; my question is, what does this scale bar actually mean? It surely can't be difference in the number of SNPs, but is it actually the measure of dissimilarity between individuals?

Many thanks

Answer 1

[David W]

It's the distance measure that you used with dist.gene, from the inline help (?dist.gene) the default is

...the distance d between two individuals is the number of loci for which they differ...