Question: splitting bootstrapping analysis in raxml
0
gravatar for Lille My
2.3 years ago by
Lille My30
Lille My30 wrote:

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!

raxml bootstrapping phylogeny • 631 views
ADD COMMENTlink modified 2.3 years ago by h.mon26k • written 2.3 years ago by Lille My30
0
gravatar for h.mon
2.3 years ago by
h.mon26k
Brazil
h.mon26k wrote:

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.

ADD COMMENTlink written 2.3 years ago by h.mon26k

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?

ADD REPLYlink written 2.3 years ago by Lille My30

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

ADD REPLYlink written 2.3 years ago by h.mon26k
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