Question: What does mean branch length of Maximum likelihood tree?
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gravatar for nakanomasayuki265
23 months ago by
nakanomasayuki26550 wrote:

I am beginner of informatics and population genetics. I made Maximum likelihood tree using RAxML. I have a question. What does mean branch length of Maximum likelihood tree? What does mean scale bar?

sequence • 2.5k views
ADD COMMENTlink modified 23 months ago by Jean-Karim Heriche18k • written 23 months ago by nakanomasayuki26550
1
gravatar for Jean-Karim Heriche
23 months ago by
EMBL Heidelberg, Germany
Jean-Karim Heriche18k wrote:

Typically, branch length represents the number of substitutions per site. You may want to have a look at this tutorial on reading phylogenetic trees.

ADD COMMENTlink written 23 months ago by Jean-Karim Heriche18k

Thank you. My tree have branch length above 1. Can substitutions per site exceed 1 ?

ADD REPLYlink written 23 months ago by nakanomasayuki26550

Given enough time, each site can mutate multiple times. Though you will not see substitutions beyond 3/4 in your data. See also Jukes-Cantor.

ADD REPLYlink modified 23 months ago • written 23 months ago by kloetzl1.0k

Yes, you can get very long branches for a variety of reasons like missing data in some part of the multiple alignment or the choice of substitution model.

ADD REPLYlink written 23 months ago by Jean-Karim Heriche18k
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