3 files changed, 143 insertions, 10 deletions

diff --git a/biology/t_coffee/Makefile b/biology/t_coffee/Makefile
index 94c762f9452b..6f7150983944 100644
--- a/biology/t_coffee/Makefile
+++ b/biology/t_coffee/Makefile
@@ -7,7 +7,7 @@
 #
 
 PORTNAME=	t_coffee
-PORTVERSION=	3.27
+PORTVERSION=	4.96
 CATEGORIES=	biology
 MASTER_SITES=	http://www.tcoffee.org/Packages/
 DISTNAME=	T-COFFEE_distribution_Version_${PORTVERSION}
diff --git a/biology/t_coffee/distinfo b/biology/t_coffee/distinfo
index cde81b662a5c..21e99a193bfb 100644
--- a/biology/t_coffee/distinfo
+++ b/biology/t_coffee/distinfo
@@ -1,3 +1,3 @@
-MD5 (T-COFFEE_distribution_Version_3.27.tar.gz) = 747d907f4b87e07d7b1e670a2b263e23
-SHA256 (T-COFFEE_distribution_Version_3.27.tar.gz) = ffb7920919b24a6144492bec71580cda8a3ef4698acf762f76ebadfcae9aa01a
-SIZE (T-COFFEE_distribution_Version_3.27.tar.gz) = 1295287
+MD5 (T-COFFEE_distribution_Version_4.96.tar.gz) = ce40b2654663b7c22c1c8427fb5e32db
+SHA256 (T-COFFEE_distribution_Version_4.96.tar.gz) = 49181acd69a5723fd5b11f579b1efe685b5289bf187985b25b40c514b0af0213
+SIZE (T-COFFEE_distribution_Version_4.96.tar.gz) = 2863327
diff --git a/biology/t_coffee/pkg-plist b/biology/t_coffee/pkg-plist
index 0f08b4e45ba9..a151b2311dab 100644
--- a/biology/t_coffee/pkg-plist
+++ b/biology/t_coffee/pkg-plist
@@ -3,16 +3,63 @@ bin/t_coffee
 %%PORTDOCS%%%%DOCSDIR%%/aln_compare.doc.txt
 %%PORTDOCS%%%%DOCSDIR%%/seq_reformat.doc.txt
 %%PORTDOCS%%%%DOCSDIR%%/t_coffee.pdf
-%%PORTDOCS%%%%DOCSDIR%%/t_coffee_doc.doc
-%%PORTDOCS%%%%DOCSDIR%%/t_coffee_doc.pdf
-%%PORTDOCS%%%%DOCSDIR%%/t_coffee_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.3752
+%%EXAMPLESDIR%%/error_report.T-COFFEE
+%%EXAMPLESDIR%%/g0.aln
+%%EXAMPLESDIR%%/x
+%%EXAMPLESDIR%%/g10.aln
+%%EXAMPLESDIR%%/g15.aln
+%%EXAMPLESDIR%%/g5.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%%/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
@@ -22,13 +69,19 @@ bin/t_coffee
 %%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%%/struc1.pdb
 %%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
@@ -36,22 +89,102 @@ bin/t_coffee
 %%EXAMPLESDIR%%/sample_seq1.aln
 %%EXAMPLESDIR%%/sample_seq1.fasta
 %%EXAMPLESDIR%%/sample_seq2.fasta
+%%EXAMPLESDIR%%/seq.fas
 %%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.g15.html
+%%EXAMPLESDIR%%/sproteases_small.html
+%%EXAMPLESDIR%%/struc1.pdb
+%%EXAMPLESDIR%%/sproteases_small.mafft
+%%EXAMPLESDIR%%/sproteases_small.mcoffee
+%%EXAMPLESDIR%%/sproteases_small.muscle
+%%EXAMPLESDIR%%/sproteases_small.ph
+%%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%%/struc2.pdb
 %%EXAMPLESDIR%%/struc3.pdb
 %%EXAMPLESDIR%%/struc4.pdb
+%%EXAMPLESDIR%%/struc5.pdb
+%%EXAMPLESDIR%%/struc6.pdb
+%%EXAMPLESDIR%%/struc7.pdb
+%%EXAMPLESDIR%%/struc8.pdb
+%%EXAMPLESDIR%%/sv.aln
+%%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
-@dirrmtry %%DOCSDIR%%
+%%PORTDOCS%%@dirrmtry %%DOCSDIR%%
 @dirrmtry %%EXAMPLESDIR%%
 @dirrm %%DATADIR%%/html
 @dirrmtry %%DATADIR%%