ML search: One step
raxmlHPC-PTHREADS.exe -T 2 -f d -m GTRGAMMA -N 1 -O -p 362  -s infile.txt  -n infile.tre  -w  "C:/Users/mmiller/Desktop/cipres/raxmlgui/DNA_2/"      
raxmlHPC-PTHREADS.exe -T 2 -f a -x 59   -m GTRGAMMA -p 783 -N 100  -s  "C:/Users/mmiller/Desktop/cipres/raxmlgui/DNA_constraint/infile.txt"  -n infile.tre  -O -w  "C:/Users/mmiller/Desktop/cipres/raxmlgui/DNA_constraint/"    
 exit

RAXMLHPC_TGB
infile_ - Primary Input File
runtime_ - Float - Maximum Hours to Run (click here for help setting this correctly)
datatype_ - Excl - Sequence Type
outgroup_ - String - Outgroup (one or more comma-separated outgroups, see comment for syntax)
constraint_ - InFile - Constraint (-g)
binary_backbone_ - InFile - Binary Backbone (-r)
partition_ - InFile - Use a mixed/partitioned model? (-q)
exclude_file_ - InFile - Create an input file that excludes the range of positions specifed in this file (-E)
invariable_ - Excl - Estimate proportion of invariable sites (GTRGAMMA + I)
prot_matrix_spec_ - Excl - Protein Substitution Matrix
empirical_ - Excl - Use empirical base frequencies?
mlsearch_ - Switch - Find best tree using maximum likelihood search
use_bootstopping_ - Switch - Let RAxML halt bootstrapping automatically (HIGHLY recommended)
printbrlength_ - Switch - Print branch lengths (-k)
all_outputfiles_ - Results -

Job is OK, command line is 
'raxmlHPC-HYBRID   -m GTRGAMMA -N 1 -O -p 362 -n infile  -s infile'