Hi Everyone,

I am new to phylogenetics and using RAXML to generate my phylogenetic trees. I did bootstrapping (1000) to get the support values on the best ML tree. I get two output files: one is the ML best tree and the other one contains the bootstrap values. Which tree I should use as an output? They both look pretty similar.

Thanks, RT
<p>They will be identical, except the bootstrapped tree will have support values (generated through bootstrap resampling).</p>

<p>For systematic inference, a tree without support values is more-or-less meaningless, as you might have bipartitions that are not well-supported yet still present in your consensus tree.</p>

<p>For comparative phylogenetic methods, you ought to 1) use the best-supported tree or 2) use a distribution of trees.</p>
