I would like to construct a very large tree using raxml. Last time I ran raxml on the data the server had to reboot and all data was lost.
Is there a way to conduct the analysis step by step, saving all of the trees along the way?
If I am not mistaken, if you do not perform bootstrap, RAxML has a checkpoint option - you can resume in case of crashes. After searching for the best tree, you can perform the bootstraps: RAxML saves each bootstrap as it progresses, and it is easy to "resume" the bootstrap searches.