I know that this is an elementary question, but it's one that I've been struggling to find the answer to.
When RAxML calculates branch lengths on default settings, what exactly do the numbers it produces mean? I gather that it's a measure of genetic distance between two nodes, but how is that calculated and what are the units of the values produced. I think that's what I really want; the units of the branch lengths.
Here is the code I am using, in case I'm inadvertently changing the RAxML settings:
raxmlHPC -s alignment.afa -n output -m GTRCAT -f a -x 1234 -N 100 -p 1234
And here is an example of a tree I have produced.
Is there a setting available in RAxML to label branches with the absolute number of variants, rather than the genetic differences? If so I'd be very grateful if someone could provide the argument for it.
Many thanks in advance.