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Maximum Likelihood Inference

What is the fastest way of infering phylogeny by Maximum Likelihood with bootstrap? I tried to use PAUP* 4.0, but making some calculations, it would take more than a week...

The alignment has 50 sequences of ~7000 nt each.

phylogeny likelihood

Did you give a try to RAxML already?

I tried RAxML on the CIPRES server. The job was killed after 10 hours running.

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