Estimate branch length with a fixed tree

[shaohong feng]

Hi,

I have an 1kb alignment and a phylogenetic tree. It is a Newick tree without branch length.

I would like to use RAxML to estimate the branch length of this fixed tree.

Is the following command feasible? Or is there a better way?

./raxmlHPC -f n -m GTRGAMMA -s ./alignment.fa -n I1 -z ./fixed.tree

thanks

[Alexandros Stamatakis]

I'd use:

./raxmlHPC -f e -m GTRGAMMA -s ./alignment.fa -n I1 -t ./fixed.tree


If it's just one fixed tree.

Also note that standard RAxML is not supported any more and you should
switch to RAxML-NG:

https://github.com/amkozlov/raxml-ng

Alexis

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--
Alexandros (Alexis) Stamatakis

Research Group Leader, Heidelberg Institute for Theoretical Studies
Full Professor, Dept. of Informatics, Karlsruhe Institute of Technology
Affiliated Scientist, Evolutionary Genetics and Paleogenomics (EGP) lab,
Institute of Molecular Biology and Biotechnology, Foundation for
Research and Technology Hellas

www.exelixis-lab.org

[Alexey Kozlov]

please use raxml-ng --evaluate command:

https://github.com/amkozlov/raxml-ng/wiki/Tutorial#tree-likelihood-evaluation