What does mean branch length of Maximum likelihood tree?
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7.1 years ago

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?

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7.1 years ago

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

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

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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.

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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.

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