bin/t_coffee %%PORTDOCS%%%%DOCSDIR%%/README4T-COFFEE %%PORTDOCS%%%%DOCSDIR%%/aln_compare.doc.txt %%PORTDOCS%%%%DOCSDIR%%/seq_reformat.doc.txt %%PORTDOCS%%%%DOCSDIR%%/t_coffee_technical.doc %%PORTDOCS%%%%DOCSDIR%%/t_coffee_technical.htm %%PORTDOCS%%%%DOCSDIR%%/t_coffee_technical.txt %%PORTDOCS%%%%DOCSDIR%%/t_coffee_tutorial.doc %%PORTDOCS%%%%DOCSDIR%%/t_coffee_tutorial.htm %%PORTDOCS%%%%DOCSDIR%%/t_coffee_tutorial.txt %%EXAMPLESDIR%%/2seqs.fas %%EXAMPLESDIR%%/3d.aln %%EXAMPLESDIR%%/3d.dnd %%EXAMPLESDIR%%/3d.fasta %%EXAMPLESDIR%%/3d.html %%EXAMPLESDIR%%/3d_sample2.fasta %%EXAMPLESDIR%%/3d_sample3.fasta %%EXAMPLESDIR%%/3d_sample4.aln %%EXAMPLESDIR%%/b30.aln %%EXAMPLESDIR%%/block1.aln %%EXAMPLESDIR%%/block2.aln %%EXAMPLESDIR%%/cache %%EXAMPLESDIR%%/charge_relay_lib.tc_lib %%EXAMPLESDIR%%/clustalw_method.tc_method %%EXAMPLESDIR%%/combined_aln.aln %%EXAMPLESDIR%%/combined_aln.aln.aln %%EXAMPLESDIR%%/combined_aln.aln.html %%EXAMPLESDIR%%/command_line.txt %%EXAMPLESDIR%%/error_report.T-COFFEE %%EXAMPLESDIR%%/g0.aln %%EXAMPLESDIR%%/x %%EXAMPLESDIR%%/g10.aln %%EXAMPLESDIR%%/g15.aln %%EXAMPLESDIR%%/g5.aln %%EXAMPLESDIR%%/kinases.aln %%EXAMPLESDIR%%/marna.tc_lib %%EXAMPLESDIR%%/new_profile1_pdb1.aln %%EXAMPLESDIR%%/new_profile1_pdb1.html %%EXAMPLESDIR%%/newprf.aln %%EXAMPLESDIR%%/newprf.html %%EXAMPLESDIR%%/p120.aln %%EXAMPLESDIR%%/p250 %%EXAMPLESDIR%%/p350.aln %%EXAMPLESDIR%%/prf1.aln %%EXAMPLESDIR%%/prf1.dnd %%EXAMPLESDIR%%/prf1.fasta %%EXAMPLESDIR%%/prf2.aln %%EXAMPLESDIR%%/prf2.dnd %%EXAMPLESDIR%%/prf2.fasta %%EXAMPLESDIR%%/prf3.aln %%EXAMPLESDIR%%/prf3.fasta %%EXAMPLESDIR%%/profile1_pdb1.aln %%EXAMPLESDIR%%/profile1_pdb1.fasta %%EXAMPLESDIR%%/profile1_pdb1.html %%EXAMPLESDIR%%/seq.fas %%EXAMPLESDIR%%/profile1_pdb1_1.aln %%EXAMPLESDIR%%/profile1_pdb1_1.html %%EXAMPLESDIR%%/profile2_pdb2.aln %%EXAMPLESDIR%%/profile2_pdb2.dnd %%EXAMPLESDIR%%/profile2_pdb2.fasta %%EXAMPLESDIR%%/profile2_pdb2.html %%EXAMPLESDIR%%/sample_aln1.aln %%EXAMPLESDIR%%/sample_aln1.dnd %%EXAMPLESDIR%%/sample_aln1.fasta %%EXAMPLESDIR%%/sample_aln1.tc_lib %%EXAMPLESDIR%%/sample_aln1_1.aln %%EXAMPLESDIR%%/sample_aln1_2.aln %%EXAMPLESDIR%%/sample_aln2.aln %%EXAMPLESDIR%%/sample_aln2.fasta %%EXAMPLESDIR%%/sample_aln2.msf %%EXAMPLESDIR%%/sample_aln3.aln %%EXAMPLESDIR%%/sample_aln4.aln %%EXAMPLESDIR%%/sample_aln5.aln %%EXAMPLESDIR%%/sample_aln6.aln %%EXAMPLESDIR%%/sample_aln6.cache %%EXAMPLESDIR%%/sample_aln6.html %%EXAMPLESDIR%%/sample_aln7.aln %%EXAMPLESDIR%%/sample_aln7.cache_aln %%EXAMPLESDIR%%/sample_dnaseq1.fasta %%EXAMPLESDIR%%/sample_lib1.mocca_lib %%EXAMPLESDIR%%/sample_lib1.tc_lib %%EXAMPLESDIR%%/sample_lib2.tc_lib %%EXAMPLESDIR%%/sample_lib3.tc_lib %%EXAMPLESDIR%%/sample_lib4.tc_lib02 %%EXAMPLESDIR%%/sample_lib5.tc_lib %%EXAMPLESDIR%%/sample_list1.lib_list %%EXAMPLESDIR%%/sample_param_file.param %%EXAMPLESDIR%%/sample_profile1.aln %%EXAMPLESDIR%%/sample_profile2.aln %%EXAMPLESDIR%%/sample_rnaseq1.fasta %%EXAMPLESDIR%%/sample_seq1.aln %%EXAMPLESDIR%%/sv.aln %%EXAMPLESDIR%%/sample_seq1.fasta %%EXAMPLESDIR%%/sample_seq2.fasta %%EXAMPLESDIR%%/sample_seq3.fasta %%EXAMPLESDIR%%/sample_seq4.fasta %%EXAMPLESDIR%%/sample_seq5.fasta %%EXAMPLESDIR%%/sample_seq6.fasta %%EXAMPLESDIR%%/sample_seq7.fasta %%EXAMPLESDIR%%/sample_seq8.seq %%EXAMPLESDIR%%/sample_tree.dnd %%EXAMPLESDIR%%/sample_tree2.dnd %%EXAMPLESDIR%%/sample_tree3.dnd %%EXAMPLESDIR%%/sproteases.small %%EXAMPLESDIR%%/sproteases.small.blosum62mt.sim_file %%EXAMPLESDIR%%/sproteases1_small.aln %%EXAMPLESDIR%%/sproteases1_small.dnd %%EXAMPLESDIR%%/sproteases1_small.fasta %%EXAMPLESDIR%%/sproteases2_small.aln %%EXAMPLESDIR%%/sproteases2_small.dnd %%EXAMPLESDIR%%/sproteases2_small.fasta %%EXAMPLESDIR%%/sproteases_chain.fasta %%EXAMPLESDIR%%/sproteases_large.aln %%EXAMPLESDIR%%/sproteases_large.code_name %%EXAMPLESDIR%%/sproteases_large.coded.fasta %%EXAMPLESDIR%%/sproteases_large.dnd %%EXAMPLESDIR%%/sproteases_large.fasta %%EXAMPLESDIR%%/sproteases_large.fasta.blosum62mt.sim2_file %%EXAMPLESDIR%%/sproteases_large.fasta.blosum62mt.sim_file %%EXAMPLESDIR%%/sproteases_large.fasta~ %%EXAMPLESDIR%%/sproteases_large.html %%EXAMPLESDIR%%/sproteases_large.muscle %%EXAMPLESDIR%%/sproteases_large_muscle_trim.aln %%EXAMPLESDIR%%/sproteases_oneseq.fasta %%EXAMPLESDIR%%/sproteases_pair.fasta %%EXAMPLESDIR%%/sproteases_small.aln %%EXAMPLESDIR%%/sproteases_small.b62_aln %%EXAMPLESDIR%%/sproteases_small.cw_aln %%EXAMPLESDIR%%/sproteases_small.dnd %%EXAMPLESDIR%%/sproteases_small.expresso %%EXAMPLESDIR%%/sproteases_small.fasta %%EXAMPLESDIR%%/sproteases_small.g0.aln %%EXAMPLESDIR%%/sproteases_small.g0.cw_aln %%EXAMPLESDIR%%/sproteases_small.g10.cw_aln %%EXAMPLESDIR%%/sproteases_small.g10.html %%EXAMPLESDIR%%/sproteases_small.g10.score_ascii %%EXAMPLESDIR%%/sproteases_small.g15.cw_aln %%EXAMPLESDIR%%/sproteases_small.ph %%EXAMPLESDIR%%/sproteases_small.g15.html %%EXAMPLESDIR%%/sproteases_small.html %%EXAMPLESDIR%%/sproteases_small.mafft %%EXAMPLESDIR%%/sproteases_small.mcoffee %%EXAMPLESDIR%%/sproteases_small.muscle %%EXAMPLESDIR%%/sproteases_small.probcons %%EXAMPLESDIR%%/sproteases_small.score_ascii %%EXAMPLESDIR%%/sproteases_small.score_html %%EXAMPLESDIR%%/sproteases_small.tc_aln %%EXAMPLESDIR%%/sproteases_small.tc_aln.aln %%EXAMPLESDIR%%/sproteases_small.tc_aln.html %%EXAMPLESDIR%%/sproteases_small.template_file %%EXAMPLESDIR%%/sproteases_small_dna.fasta %%EXAMPLESDIR%%/struc1.pdb %%EXAMPLESDIR%%/struc2.pdb %%EXAMPLESDIR%%/struc3.pdb %%EXAMPLESDIR%%/struc4.pdb %%EXAMPLESDIR%%/struc5.pdb %%EXAMPLESDIR%%/struc6.pdb %%EXAMPLESDIR%%/struc7.pdb %%EXAMPLESDIR%%/struc8.pdb %%EXAMPLESDIR%%/sv.dnd %%EXAMPLESDIR%%/sv.fasta %%EXAMPLESDIR%%/sv.html %%EXAMPLESDIR%%/sv.maln %%EXAMPLESDIR%%/t_coffee.log %%EXAMPLESDIR%%/template_file.template %%EXAMPLESDIR%%/template_file6.template %%EXAMPLESDIR%%/template_file7.template %%EXAMPLESDIR%%/test.lib %%EXAMPLESDIR%%/test.tc_lib %%EXAMPLESDIR%%/test_lib.tc_lib %%EXAMPLESDIR%%/three_pdb.aln %%EXAMPLESDIR%%/three_pdb.dnd %%EXAMPLESDIR%%/three_pdb.fasta %%EXAMPLESDIR%%/three_pdb_two_seq.aln %%EXAMPLESDIR%%/three_pdb_two_seq.dnd %%EXAMPLESDIR%%/three_pdb_two_seq.fasta %%EXAMPLESDIR%%/three_pdb_two_seq.fasta~ %%EXAMPLESDIR%%/tlara_libraries.tar %%EXAMPLESDIR%%/tlara_tRNA_aln10.output %%EXAMPLESDIR%%/tlara_tRNA_aln50.output %%EXAMPLESDIR%%/tlara_tRNA_aln51.output %%EXAMPLESDIR%%/tmp_file_for_extract_from_pdb169168.1 %%EXAMPLESDIR%%/tmp_file_for_extract_from_pdb89508.1 %%EXAMPLESDIR%%/two_profiles.template_file %%DATADIR%%/license.txt %%DATADIR%%/html/t_coffee.html %%DATADIR%%/html/t_coffee4html.cgi %%PORTDOCS%%@dirrmtry %%DOCSDIR%% @dirrmtry %%EXAMPLESDIR%% @dirrm %%DATADIR%%/html @dirrmtry %%DATADIR%%