Bootstrap support for the final RAxML_bestTree.project_name_refined.tre

[Ilia Burgsdorf]

Dear all,

I am using PHYLOPHAN2. 

The preliminary tree produced by FASTTREEMP (project_name.tre) has the bootstrap support. I was wondering if I can get bootstrap support for the final tree (RAxML_bestTree.project_name_refined.tre)? Can I just add the bootstrap parameters to the configuration file?  

Configuration file for RAXML:

[tree2]

program_name = raxmlHPC-PTHREADS-SSE3

params = -p 1989 -m PROTCATLG

database = -t

input = -s

output_path = -w

output = -n

version = -v

command_line = #program_name# #params# #threads# #database# #output_path# #input# #output#

threads = -T

Best regards,

Ilia

[Francesco Asnicar]

Dear Ilia,

Thanks for using PhyloPhlAn. Be careful that the FastTree support values are not "real" bootstrap values as general intended, you can get more info about the support value calculation in FastTree from here: http://www.microbesonline.org/fasttree/

Yes, definitely you can add to the RAxML params in the configuration file the bootstrap calculation.

Please, let me know if something is not clear.

Many thanks,

Francesco

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