Branch Length
What's the meaning of branch length? For example, 2 paralogs with a distance of 1.966087, what does it mean?
Thank you
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1 Posted by Thomas Walsh on 20 Jun, 2025 03:20 PM
Hello Noga,
My apologies for the delay in the response to your query.
A colleague has shared the following answer to your question.
As described in the TreeFam documentation, the branch lengths of the final phylogenetic trees are calculated based on the multiple alignments of the DNA sequences of the genes in question under the HKY substitution model which takes into account multiple substitutions, transition/transversion ratio and unequal base frequencies. The substitution models are set up in a way that the unit of the branch lengths is “one nucleotide substitution per nucleotide site“. If the estimated branch length of 1.9 means that the sites on average experienced this number of substitutions on that branch of the phylogenetic tree. Note, that this number can be higher than 1, as the substitution model accounts for the possibility of multiple “hits” per site.
The branch length is only an estimate of “sequence divergence“ and not actual time, since without knowing the rate of substitutions per year (or generation) and assuming a form of a molecular clock, the actual time of evolution corresponding to the branch length cannot be estimated.
I hope this answers your question. For future queries, please reach out to us via the EBI helpdesk form ( https://www.ebi.ac.uk/about/contact/support/ ) under the topic, “TreeFam - database of animal gene trees”.