9 files changed, 438 insertions, 0 deletions

diff --git a/biology/Makefile b/biology/Makefile
index b1798bf04f78..ead96e624098 100644
--- a/biology/Makefile
+++ b/biology/Makefile
@@ -44,6 +44,7 @@
     SUBDIR += seaview
     SUBDIR += seqio
     SUBDIR += sim4
+    SUBDIR += t_coffee
     SUBDIR += tinker
     SUBDIR += treeviewx
     SUBDIR += xdrawchem
diff --git a/biology/t_coffee/Makefile b/biology/t_coffee/Makefile
new file mode 100644
index 000000000000..f1d3ddb63800
--- /dev/null
+++ b/biology/t_coffee/Makefile
@@ -0,0 +1,56 @@
+# New ports collection makefile for:	t_coffee
+# Date created:		27 June 2001
+# Whom:	      		Johann Visagie <wjv@FreeBSD.org>
+#
+# $FreeBSD$
+#
+
+PORTNAME=	t_coffee
+PORTVERSION=	1.37
+CATEGORIES=	biology
+MASTER_SITES=	http://igs-server.cnrs-mrs.fr/~cnotred/Packages/
+DISTNAME=	T-COFFEE_distribution
+
+MAINTAINER=	wjv@FreeBSD.org
+
+BUILD_DEPENDS=	clustalw:${PORTSDIR}/biology/clustalw
+RUN_DEPENDS=	${BUILD_DEPENDS}
+
+WRKSRC=		${WRKDIR}/${DISTNAME}_Version_${PORTVERSION}
+BUILD_WRKSRC=	${WRKSRC}/t_coffee_source
+MAKE_ENV=	MV=${MV} USER_BIN=${LOCALBASE}/bin \
+	  	CLUSTALW_4_TCOFFEE=${LOCALBASE}/bin/clustalw
+MAKEFILE=	makefile
+PKGMESSAGE=	${WRKDIR}/pkg-message
+
+post-build:
+	@ cd ${WRKSRC}/lalign && ${SETENV} ${MAKE_ENV} ${MAKE} \
+	  ${MAKE_FLAGS} ${MAKEFILE} ${MAKE_ARGS} ${ALL_TARGET}
+
+.include <bsd.port.pre.mk>
+
+do-install:
+.for binfile in t_coffee_source/t_coffee lalign/lalign2list
+	@ ${INSTALL_PROGRAM} ${WRKSRC}/${binfile} ${PREFIX}/bin
+.endfor
+.for scriptfile in extract_from_pdb mocca
+	@ ${INSTALL_SCRIPT} ${WRKSRC}/bin/${scriptfile} ${PREFIX}/bin
+.endfor
+
+post-install:
+	@ ${MKDIR} ${DATADIR}
+	@ ${INSTALL_DATA} ${WRKSRC}/html/* ${DATADIR}
+.if !defined(NOPORTDOCS)
+	@ ${MKDIR} ${DOCSDIR}
+	@ ${INSTALL_DATA} ${WRKSRC}/doc/* ${DOCSDIR}
+	@ ${MKDIR} ${EXAMPLESDIR}
+	@ ${RMDIR} ${WRKSRC}/example/aln 2>/dev/null || ${TRUE}
+	@ cd ${WRKSRC}/example && find * \
+	  | cpio --quiet -pdum -R ${SHAREOWN}:${SHAREGRP} ${EXAMPLESDIR}
+	@ ${SED} -e 's#%%DATADIR%%#${DATADIR}#' ${.CURDIR}/pkg-message \
+	  > ${PKGMESSAGE}
+.if !defined(BATCH)
+	@ ${CAT} ${PKGMESSAGE}
+.endif
+.endif
+.include <bsd.port.post.mk>
diff --git a/biology/t_coffee/distinfo b/biology/t_coffee/distinfo
new file mode 100644
index 000000000000..62e86cceea4c
--- /dev/null
+++ b/biology/t_coffee/distinfo
@@ -0,0 +1 @@
+MD5 (T-COFFEE_distribution.tar.gz) = a947c75871f56e83ccc1e8444495330a
diff --git a/biology/t_coffee/files/patch-lalign-makefile b/biology/t_coffee/files/patch-lalign-makefile
new file mode 100644
index 000000000000..4128d3cd6b0f
--- /dev/null
+++ b/biology/t_coffee/files/patch-lalign-makefile
@@ -0,0 +1,37 @@
+--- lalign/makefile.orig	Wed Jun 13 03:05:02 2001
++++ lalign/makefile	Wed Jun 27 17:29:56 2001
+@@ -4,14 +4,14 @@
+ # use the compiler option that invokes signed char's.
+ #
+ #sun (bsd)
+-CC= cc
++#CC= cc
+ # for MIPS: CFLAGS= -O -DUNIX -DBIGMEM -DSFCHAR="':'" -signed 
+-CFLAGS= -O -DUNIX -DBIGMEM -DSFCHAR="':'"
++#CFLAGS= -O -DUNIX -DBIGMEM -DSFCHAR="':'"
+ LFLAGS=  -o
+ #NRAND= nrand
+ #IBM RS/6000
+-NRAND= nrand48
+-RANFLG= -DRAND32
++#NRAND= nrand48
++#RANFLG= -DRAND32
+ #HZ=60 for sun, mips, 100 for rs/6000, SGI
+ HZ=60
+ 
+@@ -25,14 +25,13 @@
+ 
+ lalign2list : lalign.o pam.o lsim.o lgetaa.o ndispn.o time.o
+ 	$(CC) lalign.o pam.o lsim.o lgetaa.o ndispn.o time.o $(LFLAGS) lalign2list
+-	mv lalign2list $(USER_BIN)/lalign2list
+ lalign.o : lalign.c upam.gbl
+ pam.o : uascii.gbl upam.gbl
+ lsim.o : lsim.c zzgmata.gbl upam.gbl
+ 	$(CC)  $(CFLAGS) -c lsim.c
+ lgetaa.o : nxgetaa.c upam.gbl uascii.gbl  altlib.h
+ 	$(CC) $(CFLAGS) -DNOLIB -c nxgetaa.c
+-	mv nxgetaa.o lgetaa.o
++	$(MV) nxgetaa.o lgetaa.o
+ ndispn.o : upam.gbl
+ time.o : time.c
+ 	$(CC) $(CFLAGS) -DHZ=$(HZ) -c time.c
diff --git a/biology/t_coffee/files/patch-t_coffee_source-makefile b/biology/t_coffee/files/patch-t_coffee_source-makefile
new file mode 100644
index 000000000000..58e654ff65fd
--- /dev/null
+++ b/biology/t_coffee/files/patch-t_coffee_source-makefile
@@ -0,0 +1,10 @@
+--- t_coffee_source/makefile.orig	Wed Jul 11 23:40:30 2001
++++ t_coffee_source/makefile	Fri Jan 25 15:58:01 2002
+@@ -1,7 +1,6 @@
+ CC=cc
+ t_coffee: util_constraints_list.o util_domain_constraints_list.o util_analyse_constraints_list.o aln_convertion_util.o util_declare.o hsearch.o random.o util_make_tree.o util.o reformat_struc.o reformat.o io_func.o pb_util_read_sequence.o pb_util_read_seq_util.o tree_util.o util_dp_clean_maln.o util_dp_ssec_pwaln.o util_dp_mm_nw.o util_dp_gotoh_nw.o util_dp_cdna_fasta_nw.o util_dp_generic_fasta_nw.o util_dp_fasta_nw.o util_dp_fasta_sw.o util_dp_gotoh_sw.o util_dp_est.o util_domain_dp_drivers.o util_dp_drivers.o util_domain_dp.o CUSTOM_evaluate_for_struc.o evaluate_for_struc.o evaluate_for_domain.o evaluate_dirichlet.o evaluate.o showpair.o t_coffee.o 
+ 	$(CC) -O -o t_coffee util_constraints_list.o util_domain_constraints_list.o util_analyse_constraints_list.o aln_convertion_util.o util_declare.o hsearch.o random.o util_make_tree.o util.o reformat_struc.o reformat.o io_func.o pb_util_read_sequence.o pb_util_read_seq_util.o tree_util.o util_dp_clean_maln.o util_dp_ssec_pwaln.o util_dp_mm_nw.o util_dp_gotoh_nw.o util_dp_cdna_fasta_nw.o util_dp_generic_fasta_nw.o util_dp_fasta_nw.o util_dp_fasta_sw.o util_dp_gotoh_sw.o util_dp_est.o util_domain_dp_drivers.o util_dp_drivers.o util_domain_dp.o CUSTOM_evaluate_for_struc.o evaluate_for_struc.o evaluate_for_domain.o evaluate_dirichlet.o evaluate.o showpair.o t_coffee.o  -lm
+-	mv  t_coffee  ../bin
+ 
+ all:  t_coffee
+ 
diff --git a/biology/t_coffee/pkg-comment b/biology/t_coffee/pkg-comment
new file mode 100644
index 000000000000..c0f726dcae6b
--- /dev/null
+++ b/biology/t_coffee/pkg-comment
@@ -0,0 +1 @@
+A multiple DNA or protein sequence alignment package
diff --git a/biology/t_coffee/pkg-descr b/biology/t_coffee/pkg-descr
new file mode 100644
index 000000000000..304a8fc9eb80
--- /dev/null
+++ b/biology/t_coffee/pkg-descr
@@ -0,0 +1,17 @@
+From the website:
+
+  T-Coffee is a multiple sequence alignment package. Given a set of sequences
+  (Proteins or DNA), T-Coffee generates a multiple sequence alignment.
+
+  Related publications:
+  - T-Coffee: A novel method for multiple sequence alignments.  C.Notredame,
+    D. Higgins, J. Heringa, Journal of Molecular Biology,Vol 302,
+    pp205-217,2000
+  - COFFEE: A New Objective Function For Multiple Sequence Alignmnent.
+    C.  Notredame, L. Holme and D.G. Higgins,Bioinformatics,Vol 14 (5)
+    407-422,1998
+
+Author: Cedric Notredame <cedric.notredame@europe.com>
+WWW:    http://igs-server.cnrs-mrs.fr/~cnotred/Projects_home_page/t_coffee_home_page.html
+
+-- Johann Visagie <wjv@FreeBSD.org>
diff --git a/biology/t_coffee/pkg-message b/biology/t_coffee/pkg-message
new file mode 100644
index 000000000000..780b03c483ad
--- /dev/null
+++ b/biology/t_coffee/pkg-message
@@ -0,0 +1,10 @@
+--------------------------------------------------------------------------
+
+The files required for the T-Coffee web front-end have been installed to:
+
+  %%DATADIR%%
+
+In order to use the web front-end, you will need to copy these files to
+your web server's cgi-bin directory, or a subdirectory thereof.
+
+--------------------------------------------------------------------------
diff --git a/biology/t_coffee/pkg-plist b/biology/t_coffee/pkg-plist
new file mode 100644
index 000000000000..c57ecd5e34fe
--- /dev/null
+++ b/biology/t_coffee/pkg-plist
@@ -0,0 +1,305 @@
+%%PORTDOCS%%share/doc/t_coffee/README4T-COFFEE
+%%PORTDOCS%%share/doc/t_coffee/t_coffee.pdf
+%%PORTDOCS%%share/doc/t_coffee/t_coffee_doc.doc
+%%PORTDOCS%%share/doc/t_coffee/t_coffee_doc.html
+%%PORTDOCS%%share/doc/t_coffee/t_coffee_doc.pdf
+%%PORTDOCS%%share/doc/t_coffee/t_coffee_doc.ps
+%%PORTDOCS%%share/examples/t_coffee/seq/1aab_ref1.pep
+%%PORTDOCS%%share/examples/t_coffee/seq/1aboA_ref1.pep
+%%PORTDOCS%%share/examples/t_coffee/seq/1aboA_ref2.pep
+%%PORTDOCS%%share/examples/t_coffee/seq/1ac5_ref1.pep
+%%PORTDOCS%%share/examples/t_coffee/seq/1ad2_ref1.pep
+%%PORTDOCS%%share/examples/t_coffee/seq/1ad3_ref1.pep
+%%PORTDOCS%%share/examples/t_coffee/seq/1adj_ref1.pep
+%%PORTDOCS%%share/examples/t_coffee/seq/1ag8_ref4.pep
+%%PORTDOCS%%share/examples/t_coffee/seq/1aho_ref1.pep
+%%PORTDOCS%%share/examples/t_coffee/seq/1aisB_ref4.pep
+%%PORTDOCS%%share/examples/t_coffee/seq/1ajsA_ref1.pep
+%%PORTDOCS%%share/examples/t_coffee/seq/1ajsA_ref2.pep
+%%PORTDOCS%%share/examples/t_coffee/seq/1ajsA_ref3.pep
+%%PORTDOCS%%share/examples/t_coffee/seq/1amk_ref1.pep
+%%PORTDOCS%%share/examples/t_coffee/seq/1ar1_ref4.pep
+%%PORTDOCS%%share/examples/t_coffee/seq/1ar5A_ref1.pep
+%%PORTDOCS%%share/examples/t_coffee/seq/1au7A_ref4.pep
+%%PORTDOCS%%share/examples/t_coffee/seq/1aym3_ref1.pep
+%%PORTDOCS%%share/examples/t_coffee/seq/1bbt3_ref1.pep
+%%PORTDOCS%%share/examples/t_coffee/seq/1bgl_ref1.pep
+%%PORTDOCS%%share/examples/t_coffee/seq/1ckaA_ref4.pep
+%%PORTDOCS%%share/examples/t_coffee/seq/1cpt_ref1.pep
+%%PORTDOCS%%share/examples/t_coffee/seq/1cpt_ref2.pep
+%%PORTDOCS%%share/examples/t_coffee/seq/1csp_ref1.pep
+%%PORTDOCS%%share/examples/t_coffee/seq/1csp_ref4.pep
+%%PORTDOCS%%share/examples/t_coffee/seq/1csy_ref1.pep
+%%PORTDOCS%%share/examples/t_coffee/seq/1csy_ref2.pep
+%%PORTDOCS%%share/examples/t_coffee/seq/1dlc_ref1.pep
+%%PORTDOCS%%share/examples/t_coffee/seq/1dox_ref1.pep
+%%PORTDOCS%%share/examples/t_coffee/seq/1eft_ref1.pep
+%%PORTDOCS%%share/examples/t_coffee/seq/1eft_ref5.pep
+%%PORTDOCS%%share/examples/t_coffee/seq/1ezm_ref1.pep
+%%PORTDOCS%%share/examples/t_coffee/seq/1fieA_ref1.pep
+%%PORTDOCS%%share/examples/t_coffee/seq/1fjlA_ref1.pep
+%%PORTDOCS%%share/examples/t_coffee/seq/1fkj_ref1.pep
+%%PORTDOCS%%share/examples/t_coffee/seq/1fmb_ref1.pep
+%%PORTDOCS%%share/examples/t_coffee/seq/1gdoA_ref1.pep
+%%PORTDOCS%%share/examples/t_coffee/seq/1gowA_ref1.pep
+%%PORTDOCS%%share/examples/t_coffee/seq/1gpb_ref1.pep
+%%PORTDOCS%%share/examples/t_coffee/seq/1gtr_ref1.pep
+%%PORTDOCS%%share/examples/t_coffee/seq/1havA_ref1.pep
+%%PORTDOCS%%share/examples/t_coffee/seq/1havA_ref2.pep
+%%PORTDOCS%%share/examples/t_coffee/seq/1hfh_ref1.pep
+%%PORTDOCS%%share/examples/t_coffee/seq/1hpi_ref1.pep
+%%PORTDOCS%%share/examples/t_coffee/seq/1idy_ref1.pep
+%%PORTDOCS%%share/examples/t_coffee/seq/1idy_ref2.pep
+%%PORTDOCS%%share/examples/t_coffee/seq/1idy_ref3.pep
+%%PORTDOCS%%share/examples/t_coffee/seq/1ivy_ref5.pep
+%%PORTDOCS%%share/examples/t_coffee/seq/1krn_ref1.pep
+%%PORTDOCS%%share/examples/t_coffee/seq/1lcf_ref1.pep
+%%PORTDOCS%%share/examples/t_coffee/seq/1ldg_ref1.pep
+%%PORTDOCS%%share/examples/t_coffee/seq/1led_ref1.pep
+%%PORTDOCS%%share/examples/t_coffee/seq/1lkl_ref4.pep
+%%PORTDOCS%%share/examples/t_coffee/seq/1lvl_ref1.pep
+%%PORTDOCS%%share/examples/t_coffee/seq/1lvl_ref2.pep
+%%PORTDOCS%%share/examples/t_coffee/seq/1mfa_ref4.pep
+%%PORTDOCS%%share/examples/t_coffee/seq/1mrj_ref1.pep
+%%PORTDOCS%%share/examples/t_coffee/seq/1pamA_ref1.pep
+%%PORTDOCS%%share/examples/t_coffee/seq/1pamA_ref2.pep
+%%PORTDOCS%%share/examples/t_coffee/seq/1pamA_ref3.pep
+%%PORTDOCS%%share/examples/t_coffee/seq/1ped_ref1.pep
+%%PORTDOCS%%share/examples/t_coffee/seq/1ped_ref2.pep
+%%PORTDOCS%%share/examples/t_coffee/seq/1ped_ref3.pep
+%%PORTDOCS%%share/examples/t_coffee/seq/1pfc_ref1.pep
+%%PORTDOCS%%share/examples/t_coffee/seq/1pfc_ref4.pep
+%%PORTDOCS%%share/examples/t_coffee/seq/1pgtA_ref1.pep
+%%PORTDOCS%%share/examples/t_coffee/seq/1pii_ref1.pep
+%%PORTDOCS%%share/examples/t_coffee/seq/1pkm_ref1.pep
+%%PORTDOCS%%share/examples/t_coffee/seq/1plc_ref1.pep
+%%PORTDOCS%%share/examples/t_coffee/seq/1ppn_ref1.pep
+%%PORTDOCS%%share/examples/t_coffee/seq/1pysA_ref1.pep
+%%PORTDOCS%%share/examples/t_coffee/seq/1qpg_ref5.pep
+%%PORTDOCS%%share/examples/t_coffee/seq/1r69.pep
+%%PORTDOCS%%share/examples/t_coffee/seq/1r69_ref1.pep
+%%PORTDOCS%%share/examples/t_coffee/seq/1r69_ref2.pep
+%%PORTDOCS%%share/examples/t_coffee/seq/1r69_ref3.pep
+%%PORTDOCS%%share/examples/t_coffee/seq/1rthA_ref1.pep
+%%PORTDOCS%%share/examples/t_coffee/seq/1sbp_ref1.pep
+%%PORTDOCS%%share/examples/t_coffee/seq/1sbp_ref2.pep
+%%PORTDOCS%%share/examples/t_coffee/seq/1sesA_ref1.pep
+%%PORTDOCS%%share/examples/t_coffee/seq/1taq_ref1.pep
+%%PORTDOCS%%share/examples/t_coffee/seq/1tgxA_ref1.pep
+%%PORTDOCS%%share/examples/t_coffee/seq/1tgxA_ref2.pep
+%%PORTDOCS%%share/examples/t_coffee/seq/1thm1_ref5.pep
+%%PORTDOCS%%share/examples/t_coffee/seq/1thm2_ref5.pep
+%%PORTDOCS%%share/examples/t_coffee/seq/1thm_ref1.pep
+%%PORTDOCS%%share/examples/t_coffee/seq/1tis_ref1.pep
+%%PORTDOCS%%share/examples/t_coffee/seq/1ton_ref1.pep
+%%PORTDOCS%%share/examples/t_coffee/seq/1tvxA_ref1.pep
+%%PORTDOCS%%share/examples/t_coffee/seq/1tvxA_ref2.pep
+%%PORTDOCS%%share/examples/t_coffee/seq/1ubi_ref1.pep
+%%PORTDOCS%%share/examples/t_coffee/seq/1ubi_ref2.pep
+%%PORTDOCS%%share/examples/t_coffee/seq/1ubi_ref3.pep
+%%PORTDOCS%%share/examples/t_coffee/seq/1uky_ref1.pep
+%%PORTDOCS%%share/examples/t_coffee/seq/1uky_ref2.pep
+%%PORTDOCS%%share/examples/t_coffee/seq/1uky_ref3.pep
+%%PORTDOCS%%share/examples/t_coffee/seq/1vln_ref4.pep
+%%PORTDOCS%%share/examples/t_coffee/seq/1wit_ref1.pep
+%%PORTDOCS%%share/examples/t_coffee/seq/1wit_ref2.pep
+%%PORTDOCS%%share/examples/t_coffee/seq/1wit_ref3.pep
+%%PORTDOCS%%share/examples/t_coffee/seq/1ycc_ref1.pep
+%%PORTDOCS%%share/examples/t_coffee/seq/1ycc_ref4.pep
+%%PORTDOCS%%share/examples/t_coffee/seq/1zin_ref1.pep
+%%PORTDOCS%%share/examples/t_coffee/seq/2ack_ref1.pep
+%%PORTDOCS%%share/examples/t_coffee/seq/2cba_ref1.pep
+%%PORTDOCS%%share/examples/t_coffee/seq/2cba_ref5.pep
+%%PORTDOCS%%share/examples/t_coffee/seq/2fxb_ref1.pep
+%%PORTDOCS%%share/examples/t_coffee/seq/2hsdA_ref1.pep
+%%PORTDOCS%%share/examples/t_coffee/seq/2hsdA_ref2.pep
+%%PORTDOCS%%share/examples/t_coffee/seq/2mhr_ref1.pep
+%%PORTDOCS%%share/examples/t_coffee/seq/2myr_ref1.pep
+%%PORTDOCS%%share/examples/t_coffee/seq/2myr_ref2.pep
+%%PORTDOCS%%share/examples/t_coffee/seq/2myr_ref3.pep
+%%PORTDOCS%%share/examples/t_coffee/seq/2pia_ref1.pep
+%%PORTDOCS%%share/examples/t_coffee/seq/2pia_ref2.pep
+%%PORTDOCS%%share/examples/t_coffee/seq/2pia_ref3.pep
+%%PORTDOCS%%share/examples/t_coffee/seq/2trx_ref1.pep
+%%PORTDOCS%%share/examples/t_coffee/seq/2trx_ref2.pep
+%%PORTDOCS%%share/examples/t_coffee/seq/3cyr_ref1.pep
+%%PORTDOCS%%share/examples/t_coffee/seq/3grs_ref1.pep
+%%PORTDOCS%%share/examples/t_coffee/seq/3grs_ref2.pep
+%%PORTDOCS%%share/examples/t_coffee/seq/3pmg_ref1.pep
+%%PORTDOCS%%share/examples/t_coffee/seq/451c_ref1.pep
+%%PORTDOCS%%share/examples/t_coffee/seq/4enl_ref1.pep
+%%PORTDOCS%%share/examples/t_coffee/seq/4enl_ref2.pep
+%%PORTDOCS%%share/examples/t_coffee/seq/4enl_ref3.pep
+%%PORTDOCS%%share/examples/t_coffee/seq/5ptp_ref1.pep
+%%PORTDOCS%%share/examples/t_coffee/seq/9rnt_ref1.pep
+%%PORTDOCS%%share/examples/t_coffee/seq/S51_ref5.pep
+%%PORTDOCS%%share/examples/t_coffee/seq/S52_ref5.pep
+%%PORTDOCS%%share/examples/t_coffee/seq/actin_ref1.pep
+%%PORTDOCS%%share/examples/t_coffee/seq/arp_ref1.pep
+%%PORTDOCS%%share/examples/t_coffee/seq/gal4_ref1.pep
+%%PORTDOCS%%share/examples/t_coffee/seq/glg_ref1.pep
+%%PORTDOCS%%share/examples/t_coffee/seq/kinase1_ref4.pep
+%%PORTDOCS%%share/examples/t_coffee/seq/kinase1_ref5.pep
+%%PORTDOCS%%share/examples/t_coffee/seq/kinase2_ref4.pep
+%%PORTDOCS%%share/examples/t_coffee/seq/kinase2_ref5.pep
+%%PORTDOCS%%share/examples/t_coffee/seq/kinase3_ref5.pep
+%%PORTDOCS%%share/examples/t_coffee/seq/kinase_ref1.pep
+%%PORTDOCS%%share/examples/t_coffee/seq/kinase_ref2.pep
+%%PORTDOCS%%share/examples/t_coffee/seq/kinase_ref3.pep
+%%PORTDOCS%%share/examples/t_coffee/tc_aln/1aab_ref1.t_coffee_aln10
+%%PORTDOCS%%share/examples/t_coffee/tc_aln/1aboA_ref1.t_coffee_aln10
+%%PORTDOCS%%share/examples/t_coffee/tc_aln/1aboA_ref2.t_coffee_aln10
+%%PORTDOCS%%share/examples/t_coffee/tc_aln/1ac5_ref1.t_coffee_aln10
+%%PORTDOCS%%share/examples/t_coffee/tc_aln/1ad2_ref1.t_coffee_aln10
+%%PORTDOCS%%share/examples/t_coffee/tc_aln/1ad3_ref1.t_coffee_aln10
+%%PORTDOCS%%share/examples/t_coffee/tc_aln/1adj_ref1.t_coffee_aln10
+%%PORTDOCS%%share/examples/t_coffee/tc_aln/1ag8_ref4.t_coffee_aln10
+%%PORTDOCS%%share/examples/t_coffee/tc_aln/1aho_ref1.t_coffee_aln10
+%%PORTDOCS%%share/examples/t_coffee/tc_aln/1aisB_ref4.t_coffee_aln10
+%%PORTDOCS%%share/examples/t_coffee/tc_aln/1ajsA_ref1.t_coffee_aln10
+%%PORTDOCS%%share/examples/t_coffee/tc_aln/1ajsA_ref2.t_coffee_aln10
+%%PORTDOCS%%share/examples/t_coffee/tc_aln/1ajsA_ref3.t_coffee_aln10
+%%PORTDOCS%%share/examples/t_coffee/tc_aln/1amk_ref1.t_coffee_aln10
+%%PORTDOCS%%share/examples/t_coffee/tc_aln/1ar1_ref4.t_coffee_aln10
+%%PORTDOCS%%share/examples/t_coffee/tc_aln/1ar5A_ref1.t_coffee_aln10
+%%PORTDOCS%%share/examples/t_coffee/tc_aln/1au7A_ref4.t_coffee_aln10
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