How Could We Generate A Tree With Bootstrap Value With One Command Using Raxml?

Question

[cacaucenturion]

Hi All,

I tried

raxmlHPC -m PROTCATJTT -p 12345 -b 12345 -# 100 -s $myfile -n $myname -f d

but just got multiple bootstrap trees.

Thanks!

Answer 1

[David W]

You're looking for -f a

from the manual

-f a: tell RAxML to conduct a rapid Bootstrap analysis and search for the best-scoring ML tree in one single program run. Example: raxmlHPC -f a -s alg -x 12345 -# 100 -m GTRCAT -n TEST.

But now that you have a bootstrap sample of trees you can use -f b to project the support values on to a optimum ML tree (which you can estimate separately). Again from the manual

-f b: when this is specified RAxML will draw the bipartitions using a bunch of topologies (typically bootstrapped trees) specified with -z (see below) onto a single tree topology specified by -t (typically the best-scoring ML tree). Example: raxmlHPC -f b -t ref -z trees -m GTRCAT -s alg -n TEST.

[cacaucenturion]

Thanks! But the output results do not include a best tree with bootstrap value on it. Could you tell me how I can get a tree with bootstrap value? Thanks!

[David W]

If you use -f a the tree file name RAxML_bipartions.[run_name] will be the best tree with bootstraps. For the f -b approach you first need to estimate a an optimal tree

[cacaucenturion]

Thanks a lot! I got it!