Hello everyone, I am trying to recompile the correct steps to make the majority consensus phylogeny of a maximum likelihood bootstrap tree. I would appreciate if someone could verify if these steps would be correct or if I am doing something wrong. I am processing a concatenate of amino-acids 168 taxa, 13600 characters each aprox for my project. Suggested model: JTT+I+G+F = PROTGAMMAIJTTF. I am using a cluster (using slurm job system) with access to the MPI and PTHREADS version (not hybrid).

Reference best tree (PTHREADS):

raxmlHPC-PTHREADS-SSE3 -s input_file -m PROTGRAMMAIJTTF -p 12345 -nTEST -T $SLURM_NCPUS

Bootstrap (MPI):

mpirun -n $SLURM_NTASKS raxmlHPC-MPI-SSE3 -s input_file -m PROTGRAMMAIJTTF -p 12345 -n TEST -# 10 -b 12345

Consensus tree building:

raxmlHPC -m PROTGRAMMAIJTTF -p 12345 -f b -t best_tree -z bootstrap_trees -n TEST

Thanks in advance.

Modification: I believe some persons can misunderstand the question. I am asking if the steps of getting the best tree, then bootstrapping and finally getting a consensus tree out of the las steps is the correct way to get a majority consensus tree for let´s say a publication. I already read the manual and that´s how I came out with the scripts adapted to my data, but it doesn´t specifies a workflow.