t_coffee -update
		t_coffee sample_seq1.fasta [**]
t_coffee -in= Asample_aln1.aln,Asample_aln2.aln,Asample_aln3.aln -outfile=combined_aln.aln [**]
t_coffee -infile=sample_aln1.aln -special_mode=evaluate [**]
t_coffee 3d.fasta -special_mode=3dcoffee [*#]
which wget [**]
t_coffee -other_pg mocca sample_seq1.fasta [**]

t_coffee sample_seq1.fasta [**] 
t_coffee -other_pg mocca sample_seq1.fasta [**]
	t_coffee sample_seq1.fasta

t_coffee sample_seq1.fasta sample_seq2.fasta
t_coffee sample_seq1.fasta,Ssample_aln2.aln

t_coffee -in Asample_aln1_1.aln,Asample_aln1_2.aln -outfile=combined_aln.aln 

t_coffee -profile sample_aln1.aln,sample_aln2.aln -outfile=combined_profiles.aln
t_coffee Ssample_seq1.fasta,Rsample_aln2.aln -outfile seqprofile_aln

t_coffee  Rsample_profile1.aln,Rsample_profile2.aln -special_mode=3dcoffee -outfile=aligned_prf.aln

t_coffee -in Ssample_seq1.fasta,Mfast_pair,Mlalign_id_pair [**]
t_coffee sample_seq1.fasta -in=Mem0clustalw0pairwise [**]

t_coffee -other_pg unpack_clustalw_method.tc_method [**]
t_coffee -other_pg unpack_generic_method.tc_method [**]

t_coffee sample_seq1.fasta -in=Mclustalw_method.tc_method [**]
t_coffee sample_seq1.fasta -in=Mgeneric_method.tc_method [**]
t_coffee -other_pg=unpack_tc_generic_method.pl [**]

t_coffee -in=Asample_aln1_1.aln,Asample_aln1_2.aln -outfile=combined_aln.aln [**]

t_coffee -in Asample_aln1.aln -out_lib=test_lib.tc_lib -lib_only -weight=sim_pam250mt [**]
t_coffee -in=Asample_aln1.aln,Ltest_lib.tc_lib -outfile=outaln [**]

t_coffee -in=Asample_aln1_1.aln,Asample_aln1_2.aln,Mfast_pair,Mlalign_id_pair -outfile=out_aln [**]

t_coffee sample_seq1.fasta -type=PROTEIN [**]
t_coffee sample_seq1.fasta -special_mode low_memory [**]
t_coffee  sample_seq1.fasta -in=Mslow_pair,Mlalign_id_pair -tree_mode=slow -dp_mode=myers_miller_pair_wise [**]
t_coffee sample_seq1.fasta -output=msf,fasta_aln [**]
t_coffee sample_seq1.fasta -outfile=stdout -out_lib=stdout [**]
cat sample_seq1.fasta | t_coffee -infile=stdin [**]
t_coffee sample_seq1.fasta [**]
cat sample_param_file.param  | t_coffee -parameters=stdin [**]
echo -in=Ssample_seq1.fasta,Mclustalw_pair | t_coffee -parameters=stdin [**]
t_coffee sample_seq1.fasta -run_name=guacamole [**]
t_coffee Ssample_aln1.aln [**]
t_coffee -infile=Ssample_aln1.aln [**]
t_coffee -in=Ssample_aln1.aln,Mslow_pair,Mlalign_id_pair -outfile=outaln
t_coffee sample_seq1.fasta -out_lib=sample_lib1.tc_lib -lib_only [**]
t_coffee -in=Asample_aln1.aln -out_lib=sample_lib1.tc_lib -lib_only [**]
 t_coffee -in=Asample_aln1.aln -out_lib=sample_lib1.tc_lib -lib_only -weight=1000 [**]
t_coffee -in Lsample_lib1.tc_lib Lsample_lib2.tc_lib -lib_only -out_lib=sample_lib3.tc_lib [**]
t_coffee Ssample_aln1.aln -outfile=outaln[**]
t_coffee sample_seq1.fasta -output=score_ps [**]
t_coffee sample_seq2.fasta -output=score_pdf [**]

t_coffee sample_seq1.fasta -output=clustalw,score_html,score_ps,msf [**]
t_coffee sample_aln1.aln -convert -output=gcg [**]

t_coffee -other_pg seq_reformat -in sample_aln4.aln -action +force_aln seq1 10 seq2 15 [**]

t_coffee -other_pg seq_reformat -in sample_aln4.aln -action +force_aln sample_lib4.tc_lib02 [**]
t_coffee -in Asample_seq1.aln -weight=1000 -out_lib=sample_seq1.tc_lib -lib_only [**]
t_coffee -in Ssample_seq1.fasta Lsample_seq1.tc_lib -outfile sample_seq1.aln [**]
t_coffee sample_seq1.fasta -usetree=sample_tree.dnd [**]
t_coffee sample_seq4.fasta -in Mcdna_fast_pair [**]
t_coffee sample_seq4.fasta [**]
t_coffee sample_seq1.fasta Rsample_aln2.aln -outfile tacos
t_coffee Rsample_aln1.fasta Rsample_aln2.aln -outfile tacos
t_coffee  Rsample_profile1.aln,Rsample_profile2.aln -special_mode=3dcoffee -outfile=aligne_prf.aln

t_coffee sample_seq1.fasta -output=score_html [**]

t_coffee -infile=sample_aln1_1.aln -in=Asample_aln1_2.aln -special_mode=evaluate [**]
t_coffee [**]
t_coffee -help [**]
t_coffee -help -in

t_coffee sample_seq1.fasta [**]
t_coffee Ssample_seq1.fasta [**]
t_coffee -parameters=sample_param_file.param[**]
t_coffee -infile=sample_aln1.aln -special_mode=evaluate [**]

t_coffee -infile=sample_seq1.aln -in  Lsample_lib1.tc_lib -special_mode=evaluate [**]
t_coffee -other_pg=seq_reformat [**]
t_coffee -other_pg=unpack_all [**]
t_coffee -other_pg=unpack_extract_from_pdb [**]
 	
t_coffee -other_pg=extract_from_pdb -help [**]
t_coffee -infile=sample_seq1.fasta [**]
t_coffee -in=Ssample_seq1.fasta,Asample_aln1.aln,Asample_aln2.msf,Mlalign_id_pair,Lsample_lib1.tc_lib -outfile=outaln[**]
t_coffee sample_seq1.fasta -in=Xpam250mt  -gapopen=-10  -gapext=-1 [**]
t_coffee -profile sample_aln1.aln,sample_aln2.aln -outfile=profile_aln
t_coffee -in Rsample_aln1.aln,Rsample_aln2.aln,Mslow_pair,Mlalign_id_pair -outfile=profile_aln

t_coffee sample_seq1.fasta -weight=winsim10 -out_lib=test.tc_lib [**]
t_coffee sample_seq1.fasta -weight=winsim10 -out_lib=test.tc_lib [**]
t_coffee sample_seq1.fasta -weight=1000 -out_lib=test.tc_lib [**]

t_coffee sample_seq1.fasta -tree_mode=very_fast [**]
t_coffee sample_seq1.fasta -quicktree [**]
t_coffee sample_seq1.fasta -dp_mode myers_miller_pair_wise [**]
t_coffee -in=struc1.pdb,struc2.pdb,struc3.pdb,Msap_pair
t_coffee -special_mode 3dcoffee -seq 3d_sample3.fasta -template_file template_file.template
t_coffee -in Ssample_seq1.fasta,Mlalign_rs_s_pair -out_lib=sample_lib1.mocca_lib -domain -start=10 -len=50 [**]
t_coffee -in sample_lib1.mocca_lib -domain -start=10 -len=60 [**]
t_coffee -in Lsample_lib3.tc_lib,Mlalign_rs_s_pair -domain -start=100 -len=60 [##]
t_coffee sample_seq1.fasta -output=clustalw,gcg, score_html [**]
t_coffee -other_pg seq_reformat -in sample_aln1.aln -action +lower -output clustalw [**]
t_coffee sample_seq1.fasta -evaluate_mode t_coffee_slow -output score_ascii, score_html [**]

t_coffee sample_seq1.fasta -evaluate_mode t_coffee_fast -output score_ascii, score_html [**]
t_coffee sample_seq1.fasta -evaluate_mode t_coffee_non_extended -output score_ascii, score_html [**]



