Converting file from .tre to .nwk?

Hi everyone,

I have a phylogeny file as a: .tre, and need to convert it to a .nwk. Any ideas on how to do this?


Hi @agonzales, .tre (tree) files are commonly written as .nwk (newick) format. The file name extension often as little to do with the format in this case. So, you should be good to go.

Thanks @SoilRotifer for confirming that.

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HI, @SoilRotifer the output of raxml is:

Do you know if using raxml, i can get the output with distances?
somethings like this, ?


I'm not an expert on RAxML, but I think it may be the -f x option. Does this look close?

­ - f x
compute pair­wise ML distances, ML model parameters will be estimated on an
MP starting tree or a user­defined tree passed via ­t, only allowed for
GAMMA­based models of rate heterogeneity

This option will just compute the pair-wise distances (branch lengths) between the
sequences of an alignment using a maximum likelihood estimate. To obtain a model
parameter estimate (GTR, alpha shape parameter etc.) it will initially either read in a user
specified tree (e.g., the best-known ML tree) or generate a randomized stepwise addition
parsimony starting tree if no input tree is provided. It then optimizes model parameters on
this tree and then computes all pair-wises distances.

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