Normalization of Genetic Distances (raxml -f x)

[Maiara Moro]

Hello,

I am using RAxML (command -f x and the PROTGAMMAAUTO model) to calculate genetic distances between pairs of mammalian species, based on protein sequences from orthologs for thousands of genes.

My question focuses on the subsequent analysis of this data. I would like to identify more and less conserved genes between species pairs, but I am unsure how best to normalize and interpret these genetic distances for this purpose. Specifically:

Is it best practice to normalize these distances by the length of the protein sequences, or does the way these distances are calculated obviate the need for normalization?

Any guidance on how to approach this analysis, or suggestions on best practices for interpreting genetic distances in the context of identifying gene conservation between different genes, would be greatly appreciated.

Thank you in advance for your help.

[Alexandros Stamatakis]

These distances are maximum likelihood estimates of the branch lengths
between individual sequences.

Therefore, there is no need for normalization as they correspond to the
standard interpretation of branch lengths under the phylogenetic
likelihood model which is the mean number of expected mutations per site.

Alexis

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Alexandros (Alexis) Stamatakis

ERA Chair, Institute of Computer Science, Foundation for Research and
Technology - Hellas
Research Group Leader, Heidelberg Institute for Theoretical Studies
Full Professor, Dept. of Informatics, Karlsruhe Institute of Technology

www.biocomp.gr (Crete lab)
www.exelixis-lab.org (Heidelberg lab)

[Maiara Moro]

Thank you very much, Alexis. It helped a lot!

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