Question: APE (R) package NJ tree - what's the scale?
0
gravatar for biogirl
3.9 years ago by
biogirl140
European Union
biogirl140 wrote:

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

ape neighbor-joining R phylogeny • 2.1k views
ADD COMMENTlink modified 3.9 years ago by David W4.7k • written 3.9 years ago by biogirl140
0
gravatar for David W
3.9 years ago by
David W4.7k
New Zealand
David W4.7k wrote:

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..."

 

 

 

 

ADD COMMENTlink modified 3.9 years ago • written 3.9 years ago by David W4.7k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1605 users visited in the last hour