Pairwise distances
command line:
raxmlHPC-PTHREADS.exe -T 2   -f x -n infile.tre  -s  infile.txt -p 777  -m GTRGAMMA -O 

RAXMLHPC8_XSEDE-A2AB5A07B7094403B19E213FF014DB73 (saved) produces:
raxmlHPC-PTHREADS (T 8)  -f x  -n outfile.tre -s infile.txt -m GTRGAMMA -p 777  -O

RAXMLHPC8_XSEDE
select_analysis_=fx (default is fd)
outsuffix_=outfile.tre
parsimony_seed_val_=362 (set the parsimony value for the starting tree, turned off for -f a or if a tree is supplied using treeetop)
dna_gtrcat_=GTRGAMMA (default for datatype_=dna; default for dna_gtrcat_=GTRCAT)
disable_seqcheck_=1 (sets the -O value, default is off)

Job is OK, command line is 
raxmlHPC-PTHREADS (-T 8)   -f x -n outfile.tre  -s infile.txt  -p 777 -m GTRGAMMA -O '
Test passed

select_analysis: use this to choose the main analysis. if the option is -f a, the value is fa; if -f o, fo, and so forth.

other model options:
If not DNA , set datatype_=(protein/rna/binary/multi) then set this parameter
(GTRCAT default;  prot_sub_model_=PROTGAMMA/PROTCAT; rna_model_ ;bin_model_=BINCAT/BINGAMMA; multi_model_=MULTICAT/MULTIGAMMA)
Then set sub_parameters for protein:
prot_matrix_spec_= (DAYHOFF is default)

other modifiers can be set:
invariable_= - switch - Estimate proportion of invariable sites (GTRGAMMA + I)
ascertainment_= switch -
ascertainment_corr_= excl - sets the kind of correction used
use_emp_freqs_= to use empirical frequencies, protein only 

outgroup_ - String - Outgroup (one or more comma-separated outgroups, see comment for syntax)

upload modifying files
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)

printbrlength_ - Switch - Print branch lengths (-k)