Apologies for the delay. The calculation is a majority consensus phylogeny of a maximum likelihood bootstrap, which is superimposed into a maximum likelihood phylogram. That's the tech. speak over ... the command is,
raxmlHPC -f b -m PROTGAMMAILG -n output_bootstrap.tre -t RAxML_bestTree* -z RAxML_bootstrap.result
- RAxML_bestTree* = your maximum likelihood tree without bootstraps (file is probably 1 line long)
- RAxML_bootstrap.result = your complete list of bootstraps (file is 500 lines long [or the number of bootstraps you set])
- output_bootstap.tre = final result tree, i.e. majority consensus. This file is one line long but will have with all bootstraps attached to each branch.
The calculation will take less than one minute. The code is C and very slick. Note the "RAxML_bestTree*" is probably better to write the file name in full, not truncated via the glob (*). BTW you must specify the model.
Visualising the tree You use a Mac ... so the cool tree program is figtree . Make sure when you load it you click the branch option and set it to see your bootstraps, otherwise it will not visualise them by default. You might need to re-root the tree, from memory your command specified an outgroup. It might not be the right one though and figtree will easily re-root it for you. Bootstrap values above 75% are considered robust. If you get stuck, can chat but I'm not around until this time next week (bereavement leave and loads of meetings).