- Update to 4.96
PR: 110080 Submitted by: Fernan Aguero<fernan@iib.unsam.edu.ar> (maintainer)
This commit is contained in:
Martin Wilke
parent
572ad4f218
commit
d427c1e56d
Notes:
svn2git
2021-03-31 03:12:20 +00:00
svn path=/head/; revision=186994
3 changed files with 143 additions and 10 deletions
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@ -7,7 +7,7 @@
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#
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PORTNAME= t_coffee
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PORTVERSION= 3.27
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PORTVERSION= 4.96
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CATEGORIES= biology
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MASTER_SITES= http://www.tcoffee.org/Packages/
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DISTNAME= T-COFFEE_distribution_Version_${PORTVERSION}
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@ -1,3 +1,3 @@
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MD5 (T-COFFEE_distribution_Version_3.27.tar.gz) = 747d907f4b87e07d7b1e670a2b263e23
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SHA256 (T-COFFEE_distribution_Version_3.27.tar.gz) = ffb7920919b24a6144492bec71580cda8a3ef4698acf762f76ebadfcae9aa01a
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SIZE (T-COFFEE_distribution_Version_3.27.tar.gz) = 1295287
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MD5 (T-COFFEE_distribution_Version_4.96.tar.gz) = ce40b2654663b7c22c1c8427fb5e32db
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SHA256 (T-COFFEE_distribution_Version_4.96.tar.gz) = 49181acd69a5723fd5b11f579b1efe685b5289bf187985b25b40c514b0af0213
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SIZE (T-COFFEE_distribution_Version_4.96.tar.gz) = 2863327
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@ -3,16 +3,63 @@ bin/t_coffee
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%%PORTDOCS%%%%DOCSDIR%%/aln_compare.doc.txt
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%%PORTDOCS%%%%DOCSDIR%%/seq_reformat.doc.txt
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%%PORTDOCS%%%%DOCSDIR%%/t_coffee.pdf
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%%PORTDOCS%%%%DOCSDIR%%/t_coffee_doc.doc
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%%PORTDOCS%%%%DOCSDIR%%/t_coffee_doc.pdf
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%%PORTDOCS%%%%DOCSDIR%%/t_coffee_doc.txt
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%%PORTDOCS%%%%DOCSDIR%%/t_coffee_technical.doc
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%%PORTDOCS%%%%DOCSDIR%%/t_coffee_technical.htm
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%%PORTDOCS%%%%DOCSDIR%%/t_coffee_technical.txt
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%%PORTDOCS%%%%DOCSDIR%%/t_coffee_tutorial.doc
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%%PORTDOCS%%%%DOCSDIR%%/t_coffee_tutorial.htm
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%%PORTDOCS%%%%DOCSDIR%%/t_coffee_tutorial.txt
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%%EXAMPLESDIR%%/2seqs.fas
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%%EXAMPLESDIR%%/3d.aln
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%%EXAMPLESDIR%%/3d.dnd
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%%EXAMPLESDIR%%/3d.fasta
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%%EXAMPLESDIR%%/3d.html
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%%EXAMPLESDIR%%/3d_sample2.fasta
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%%EXAMPLESDIR%%/3d_sample3.fasta
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%%EXAMPLESDIR%%/3d_sample4.aln
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%%EXAMPLESDIR%%/b30.aln
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%%EXAMPLESDIR%%/block1.aln
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%%EXAMPLESDIR%%/block2.aln
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%%EXAMPLESDIR%%/cache
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%%EXAMPLESDIR%%/charge_relay_lib.tc_lib
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%%EXAMPLESDIR%%/clustalw_method.tc_method
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%%EXAMPLESDIR%%/combined_aln.aln
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%%EXAMPLESDIR%%/combined_aln.aln.aln
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%%EXAMPLESDIR%%/combined_aln.aln.html
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%%EXAMPLESDIR%%/command_line.txt
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%%EXAMPLESDIR%%/error_report.T-COFFEE.3752
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%%EXAMPLESDIR%%/error_report.T-COFFEE
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%%EXAMPLESDIR%%/g0.aln
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%%EXAMPLESDIR%%/x
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%%EXAMPLESDIR%%/g10.aln
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%%EXAMPLESDIR%%/g15.aln
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%%EXAMPLESDIR%%/g5.aln
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%%EXAMPLESDIR%%/marna.tc_lib
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%%EXAMPLESDIR%%/new_profile1_pdb1.aln
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%%EXAMPLESDIR%%/new_profile1_pdb1.html
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%%EXAMPLESDIR%%/newprf.aln
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%%EXAMPLESDIR%%/newprf.html
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%%EXAMPLESDIR%%/p120.aln
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%%EXAMPLESDIR%%/p250
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%%EXAMPLESDIR%%/p350.aln
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%%EXAMPLESDIR%%/prf1.aln
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%%EXAMPLESDIR%%/prf1.dnd
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%%EXAMPLESDIR%%/prf1.fasta
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%%EXAMPLESDIR%%/prf2.aln
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%%EXAMPLESDIR%%/prf2.dnd
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%%EXAMPLESDIR%%/prf2.fasta
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%%EXAMPLESDIR%%/prf3.aln
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%%EXAMPLESDIR%%/prf3.fasta
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%%EXAMPLESDIR%%/profile1_pdb1.aln
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%%EXAMPLESDIR%%/profile1_pdb1.fasta
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%%EXAMPLESDIR%%/profile1_pdb1.html
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%%EXAMPLESDIR%%/profile1_pdb1_1.aln
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%%EXAMPLESDIR%%/profile1_pdb1_1.html
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%%EXAMPLESDIR%%/profile2_pdb2.aln
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%%EXAMPLESDIR%%/profile2_pdb2.dnd
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%%EXAMPLESDIR%%/profile2_pdb2.fasta
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%%EXAMPLESDIR%%/profile2_pdb2.html
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%%EXAMPLESDIR%%/sample_aln1.aln
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%%EXAMPLESDIR%%/sample_aln1.dnd
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%%EXAMPLESDIR%%/sample_aln1.fasta
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%%EXAMPLESDIR%%/sample_aln1.tc_lib
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%%EXAMPLESDIR%%/sample_aln1_1.aln
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@ -22,13 +69,19 @@ bin/t_coffee
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%%EXAMPLESDIR%%/sample_aln2.msf
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%%EXAMPLESDIR%%/sample_aln3.aln
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%%EXAMPLESDIR%%/sample_aln4.aln
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%%EXAMPLESDIR%%/sample_aln5.aln
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%%EXAMPLESDIR%%/sample_aln6.aln
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%%EXAMPLESDIR%%/sample_aln6.cache
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%%EXAMPLESDIR%%/sample_aln6.html
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%%EXAMPLESDIR%%/sample_aln7.aln
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%%EXAMPLESDIR%%/sample_aln7.cache_aln
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%%EXAMPLESDIR%%/sample_dnaseq1.fasta
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%%EXAMPLESDIR%%/struc1.pdb
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%%EXAMPLESDIR%%/sample_lib1.mocca_lib
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%%EXAMPLESDIR%%/sample_lib1.tc_lib
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%%EXAMPLESDIR%%/sample_lib2.tc_lib
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%%EXAMPLESDIR%%/sample_lib3.tc_lib
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%%EXAMPLESDIR%%/sample_lib4.tc_lib02
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%%EXAMPLESDIR%%/sample_lib5.tc_lib
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%%EXAMPLESDIR%%/sample_list1.lib_list
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%%EXAMPLESDIR%%/sample_param_file.param
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%%EXAMPLESDIR%%/sample_profile1.aln
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@ -36,22 +89,102 @@ bin/t_coffee
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%%EXAMPLESDIR%%/sample_seq1.aln
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%%EXAMPLESDIR%%/sample_seq1.fasta
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%%EXAMPLESDIR%%/sample_seq2.fasta
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%%EXAMPLESDIR%%/seq.fas
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%%EXAMPLESDIR%%/sample_seq3.fasta
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%%EXAMPLESDIR%%/sample_seq4.fasta
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%%EXAMPLESDIR%%/sample_seq5.fasta
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%%EXAMPLESDIR%%/sample_seq6.fasta
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%%EXAMPLESDIR%%/sample_seq7.fasta
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%%EXAMPLESDIR%%/sample_seq8.seq
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%%EXAMPLESDIR%%/sample_tree.dnd
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%%EXAMPLESDIR%%/sample_tree2.dnd
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%%EXAMPLESDIR%%/sample_tree3.dnd
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%%EXAMPLESDIR%%/sproteases.small
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%%EXAMPLESDIR%%/sproteases.small.blosum62mt.sim_file
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%%EXAMPLESDIR%%/sproteases1_small.aln
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%%EXAMPLESDIR%%/sproteases1_small.dnd
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%%EXAMPLESDIR%%/sproteases1_small.fasta
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%%EXAMPLESDIR%%/sproteases2_small.aln
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%%EXAMPLESDIR%%/sproteases2_small.dnd
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%%EXAMPLESDIR%%/sproteases2_small.fasta
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%%EXAMPLESDIR%%/sproteases_chain.fasta
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%%EXAMPLESDIR%%/sproteases_large.aln
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%%EXAMPLESDIR%%/sproteases_large.code_name
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%%EXAMPLESDIR%%/sproteases_large.coded.fasta
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%%EXAMPLESDIR%%/sproteases_large.dnd
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%%EXAMPLESDIR%%/sproteases_large.fasta
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%%EXAMPLESDIR%%/sproteases_large.fasta.blosum62mt.sim2_file
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%%EXAMPLESDIR%%/sproteases_large.fasta.blosum62mt.sim_file
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%%EXAMPLESDIR%%/sproteases_large.fasta~
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%%EXAMPLESDIR%%/sproteases_large.html
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%%EXAMPLESDIR%%/sproteases_large.muscle
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%%EXAMPLESDIR%%/sproteases_large_muscle_trim.aln
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%%EXAMPLESDIR%%/sproteases_oneseq.fasta
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%%EXAMPLESDIR%%/sproteases_pair.fasta
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%%EXAMPLESDIR%%/sproteases_small.aln
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%%EXAMPLESDIR%%/sproteases_small.b62_aln
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%%EXAMPLESDIR%%/sproteases_small.cw_aln
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%%EXAMPLESDIR%%/sproteases_small.dnd
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%%EXAMPLESDIR%%/sproteases_small.expresso
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%%EXAMPLESDIR%%/sproteases_small.fasta
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%%EXAMPLESDIR%%/sproteases_small.g0.aln
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%%EXAMPLESDIR%%/sproteases_small.g0.cw_aln
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%%EXAMPLESDIR%%/sproteases_small.g10.cw_aln
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%%EXAMPLESDIR%%/sproteases_small.g10.html
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%%EXAMPLESDIR%%/sproteases_small.g10.score_ascii
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%%EXAMPLESDIR%%/sproteases_small.g15.cw_aln
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%%EXAMPLESDIR%%/sproteases_small.g15.html
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%%EXAMPLESDIR%%/sproteases_small.html
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%%EXAMPLESDIR%%/struc1.pdb
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%%EXAMPLESDIR%%/sproteases_small.mafft
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%%EXAMPLESDIR%%/sproteases_small.mcoffee
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%%EXAMPLESDIR%%/sproteases_small.muscle
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%%EXAMPLESDIR%%/sproteases_small.ph
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%%EXAMPLESDIR%%/sproteases_small.probcons
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%%EXAMPLESDIR%%/sproteases_small.score_ascii
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%%EXAMPLESDIR%%/sproteases_small.score_html
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%%EXAMPLESDIR%%/sproteases_small.tc_aln
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%%EXAMPLESDIR%%/sproteases_small.tc_aln.aln
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%%EXAMPLESDIR%%/sproteases_small.tc_aln.html
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%%EXAMPLESDIR%%/sproteases_small.template_file
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%%EXAMPLESDIR%%/sproteases_small_dna.fasta
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%%EXAMPLESDIR%%/struc2.pdb
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%%EXAMPLESDIR%%/struc3.pdb
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%%EXAMPLESDIR%%/struc4.pdb
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%%EXAMPLESDIR%%/struc5.pdb
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%%EXAMPLESDIR%%/struc6.pdb
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%%EXAMPLESDIR%%/struc7.pdb
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%%EXAMPLESDIR%%/struc8.pdb
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%%EXAMPLESDIR%%/sv.aln
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%%EXAMPLESDIR%%/sv.dnd
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%%EXAMPLESDIR%%/sv.fasta
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%%EXAMPLESDIR%%/sv.html
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%%EXAMPLESDIR%%/sv.maln
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%%EXAMPLESDIR%%/t_coffee.log
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%%EXAMPLESDIR%%/template_file.template
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%%EXAMPLESDIR%%/template_file6.template
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%%EXAMPLESDIR%%/template_file7.template
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%%EXAMPLESDIR%%/test.lib
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%%EXAMPLESDIR%%/test.tc_lib
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%%EXAMPLESDIR%%/test_lib.tc_lib
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%%EXAMPLESDIR%%/three_pdb.aln
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%%EXAMPLESDIR%%/three_pdb.dnd
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%%EXAMPLESDIR%%/three_pdb.fasta
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%%EXAMPLESDIR%%/three_pdb_two_seq.aln
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%%EXAMPLESDIR%%/three_pdb_two_seq.dnd
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%%EXAMPLESDIR%%/three_pdb_two_seq.fasta
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%%EXAMPLESDIR%%/three_pdb_two_seq.fasta~
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%%EXAMPLESDIR%%/tlara_libraries.tar
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%%EXAMPLESDIR%%/tlara_tRNA_aln10.output
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%%EXAMPLESDIR%%/tlara_tRNA_aln50.output
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%%EXAMPLESDIR%%/tlara_tRNA_aln51.output
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%%EXAMPLESDIR%%/tmp_file_for_extract_from_pdb169168.1
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%%EXAMPLESDIR%%/tmp_file_for_extract_from_pdb89508.1
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%%EXAMPLESDIR%%/two_profiles.template_file
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%%DATADIR%%/license.txt
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%%DATADIR%%/html/t_coffee.html
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%%DATADIR%%/html/t_coffee4html.cgi
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@dirrmtry %%DOCSDIR%%
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%%PORTDOCS%%@dirrmtry %%DOCSDIR%%
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@dirrmtry %%EXAMPLESDIR%%
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@dirrm %%DATADIR%%/html
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@dirrmtry %%DATADIR%%
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