ML search: One step or several.

raxmlHPC-PTHREADS.exe -T 2 -f d -m PROTGAMMABLOSUM62F -N 1 -O -p 130 -o 1_Euglena_gracilis -s infile2.txt"  -n infile2.tre  
&&raxmlHPC-PTHREADS.exe -T 2 -f J -m PROTGAMMABLOSUM62F -t  RAxML_bestTree.infile2.tre"  -n sh.infile2.tre -s infile2.txt"  
 exit
 
NGBW-JOB-RAXMLHPC2_WORKFLOW-AB9148F840DE4EF78160B2261009146A  (saved)
raxmlHPC-HYBRID -s infile.txt -p 12345 -m PROTGAMMABLOSUM62F -k -O -f d -N 10 -n infile.tre 
&& raxmlHPC-PTHREADS -f J -t RAxML_bestTree.infile.tre -p 12345 -n sh.infile.tre -s infile.txt -O -m PROTGAMMABLOSUM62

RAXMLHPC2_WORKFLOW
This test:
toolId=RAXMLHPC2_WORKFLOW	   (required)
first step:
runtime_=0.50				   (default)
specify_workflow_=MLS	       (no default)
datatype_=protein              (default=dna, can be others)
prot_sub_model_=PROTGAMMA      (no default, a value for the model must be set)
prot_matrix_spec_=BLOSUM62     (default is DAYHOFF, many other options)
invariable_=				   (default is null)
ascertainment_=ASC_            (default is null; ASC_ turns on the option; invariable and asc are mutually exclusive)
use_emp_freqs_=F               (default is null, F is the other choice)
printbrlength_=1               (print branch lengths, default = 0)
outgroup_=					   (default is no outgroup)
disable_seqcheck_=1            (default is 0)
workflow step specific:
mlsearch_shlike_=1             (find sh-like values, default 0)
outsuffix_MLS_=infile          (name the output files from bootstrapping step, default=infile)
mlsearch_combine_=1            (combine the output files default=0)

Commandline is:
'raxmlHPC-HYBRID -f d -m ASC_PROTGAMMABLOSUM62F  -N 10   -O  -p 12345 -s infile.txt -n infile.tre   -k 
&& raxmlHPC-PTHREADS -f J -m ASC_PROTGAMMABLOSUM62 -t RAxML_bestTree.infile.tre -p 12345 -n sh.infile.tre -s infile.txt -O  
&& type RAxML_result.infile.tre* > combined_results.infile.tre'

test pass

dna_gtrcat_=GTRGAMMA (dataytpe -= dna by default)
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)