Re: [raxml] Raxml continue interrupted run

[Alexandros Stamatakis]

RAxML does not have a restart option.

However, since you already have the bootstraps, you can now
independently compute a couple of ML trees (see manual) and then use
these results to do post-analyses ...

Alexis

On 21.07.2015 10:44, Fang Li wrote:
> Hi all,
>
> After finished all the 100 bootstraps, our server got an emergency
> reboot. And the program stopped at " Starting ML Search ..."
>
> I tried to manually finish the rest process by using the command below:
>
> ./raxmlHPC-PTHREADS -f b -z RAxML_bootstrap.version1 -t
> best.likelihood.score.tree -m GTRCAT -n version1
>
> RAxML_bootstrap.version1 is the finished bootstraps topologies without
> branch length, and best.likelihood.score.tree is the tree with highest
> ML value in the 100 bootstraps.
>
> But it seems that RAxML need a tree with branch length when using -t.
>
> I then tried using –f x to calculate the branch length for the
> best.likelihood.score.tree but failed, the output give the pair-wise
> distance instead of the branch length.
>
> So does anyone know how to calculate the branch length for the specified
> topology?
>
> Thanks in advance!
>
> Best,
>
> Fang
>
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--
Alexandros (Alexis) Stamatakis

Research Group Leader, Heidelberg Institute for Theoretical Studies
Full Professor, Dept. of Informatics, Karlsruhe Institute of Technology
Adjunct Professor, Dept. of Ecology and Evolutionary Biology, University
of Arizona at Tucson

www.exelixis-lab.org