splitting bootstrapping analysis in raxml
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5.3 years ago
Lille My ▴ 30

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 phylogeny bootstrapping • 1.2k views
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5.3 years ago
h.mon 34k

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.

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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?

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

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