splitting bootstrapping analysis in raxml

Question

[Lille My]

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? thanks!

Answer 1

[h.mon]

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.

[Lille My]

So, if I perform the analysis as a two step process, first searching for the best tree and then doing the bootstraps? Do you by any chance remember the options to use?

[h.mon]

Sadly, no, this was many years ago. I am not even sure it would help, as I used version 7.X.X.