What does mean branch length of Maximum likelihood tree?

Question

[nakanomasayuki265]

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?

Answer 1

[Jean-Karim Heriche]

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

[nakanomasayuki265]

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

[kloetzl]

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.

[Jean-Karim Heriche]

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.