RAXML ML/Thorough Bootstrap
raxmlgui makes this command line
example: raxmlHPC-PTHREADS.exe -T 2 -b 631 -m PROTGAMMABLOSUM62F -k -p 223 -N 100 -o 1_Euglena_gracilis -s infile2.txt"  -n testR -O  
&&raxmlHPC-PTHREADS.exe -T 2 -f d -m PROTGAMMABLOSUM62F -o 1_Euglena_gracilis -s infile2.txt" -N 1 -n testB -p 730 -O 
&&raxmlHPC-PTHREADS.exe -T 2 -f b -t RAxML_bestTree.testB -z RAxML_bootstrap.testR -m PROTGAMMABLOSUM62F -s infile2.txt"  -n test.tre -O 
 exit 

NGBW-JOB-RAXMLHPC2_WORKFLOW-42680FE7CE894B5FA2B08B74DDD556B2 (saved)

raxmlHPC-HYBRID -s infile.txt -N 100 -m GTRGAMMA -p 12345 -k -O -b 787 -o mycobac_01 -n testS 
&& raxmlHPC-HYBRID -f d  -m GTRGAMMA  -s infile.txt -N 10 -n testZ -p 333 -O -o mycobac_01
&& raxmlHPC-PTHREADS -f b -t  RAxML_bestTree.testZ  -z  RAxML_bootstrap.testS  -m GTRGAMMA  -s infile.txt    -n testout  -O -o mycobac_01
~


RAXMLHPC2_WORKFLOW
This test:
toolId=RAXMLHPC2_WORKFLOW		(required)
runtime_=0.50					(default)
specify_workflow_=MLTB	       (no default)
datatype_=dna             (default=dna, can be others)
dna_gtrcat_=GTRGAMMA           (no default, a value for the model must be set)
invariable_=				   (default is null)
ascertainment_=ASC_            (default is null; ASC_ turns on the option; invariable and asc are mutually exclusive)
ascertainment_corr_=          (default is lewis, felsenstein an dstamatkis are allowed, the latter two require a file via -q) 
printbrlength_=1                (print branch lengths, default = 0)
outgroup_=					   (default is no outgroup)
disable_seqcheck_=1            (default is 0)
mulparambootstrap_seed_val_=12345 (set a seed for the -b bootstrapping option, default 12345)
outsuffix_MLTB1_=testR         (name the output files from bootstrapping step, default=testR)
parsimony_seed_val_MLTB2_=12345 (provide random seed value for MLTB sampling step, default 12345)
outsuffix_MLTB2_=testB          (name for the output files for -f d ML + thorough bootstrap workflow step 2, default=testB)
outsuffix_MLTB3_=outfile        (name for the output files of step 3 in the MLTB workflow)

we make this command line
Commandline is: 

'raxmlHPC-HYBRID -n testS -s infile.txt -o 1_Euglena_gracilis -m ASC_GTRGAMMA -N 100 -k -p 12345  -b 787 -O  --asc-corr lewis
&& raxmlHPC-HYBRID -f d  -m ASC_GTRGAMMA  -s infile.txt -N 10 -n testZ -p 333 -O -o 1_Euglena_gracilis --asc-corr lewis 
&& raxmlHPC-PTHREADS -f b -t  RAxML_bestTree.testZ  -z  RAxML_bootstrap.testS  -m ASC_GTRGAMMA  -s infile.txt    -n testout  -O --asc-corr lewis -o 1_Euglena_gracilis'
Test passed

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)