Question: Branch Lengths in RAxML
0
gravatar for rc16955
2.4 years ago by
rc1695560
rc1695560 wrote:

Hi all,

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.

raxml phylogeny • 2.0k views
ADD COMMENTlink modified 2.1 years ago by lay_050 • written 2.4 years ago by rc1695560
0
gravatar for lay_0
2.1 years ago by
lay_050
lay_050 wrote:

I believe is number of changes per site, this is probably the same question: Phylogenetic Branch Length

ADD COMMENTlink written 2.1 years ago by lay_050
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