using RAxML_Flags in final genetree pipeline
I am trying to run a bootstrap analysis in RAxML. I was trying to give it the RAxML_flags but didn't know how to specify them.
Here is what I tried with my command but it did not work:
$agalma genetree --id 6Taxa_16 --align_id 296 --raxml_flags x_12345 #_100 --model PROTGAMMAWAG --newrun --outdir ../analyses
I want to run 100 rapid bootstraps, which I would normally specify with the RAxML flags: -x 12345 -# 100
I am not sure what is the correct way of specifying them.