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