7 files changed, 175 insertions, 384 deletions

diff --git a/biology/t_coffee/Makefile b/biology/t_coffee/Makefile
index ce6bd55fd374..86b1078ecbbc 100644
--- a/biology/t_coffee/Makefile
+++ b/biology/t_coffee/Makefile
@@ -6,41 +6,33 @@
 #
 
 PORTNAME=	t_coffee
-PORTVERSION=	1.37
+PORTVERSION=	2.03
 CATEGORIES=	biology
 MASTER_SITES=	http://igs-server.cnrs-mrs.fr/~cnotred/Packages/
-DISTNAME=	T-COFFEE_distribution
+DISTNAME=	T-COFFEE_distribution_Version_${PORTVERSION}
 
-MAINTAINER=	ports@FreeBSD.org
+MAINTAINER=	fernan@iib.unsam.edu.ar
 COMMENT=	A multiple DNA or protein sequence alignment package
 
 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} ${ALL_TARGET}
+MAKE_ENV=	MV=${MV} USER_BIN=${PREFIX}/bin \
+		CLUSTALW_4_TCOFFEE=${LOCALBASE}/bin/clustalw
 
-.include <bsd.port.pre.mk>
+MAKEFILE=	makefile
+SCRIPTS=	msf_aln2fasta_aln.pl blast_aln2fasta_aln.pl \
+		fasta_aln2fasta_aln_unique_name.pl extract_from_pdb \
+		fugue_client t_coffee_dpa t_coffee_dpa2 mocca
 
 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_PROGRAM} ${WRKSRC}/bin/t_coffee ${PREFIX}/bin
+.for scriptfile in ${SCRIPTS}
 	@ ${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}
@@ -48,10 +40,6 @@ post-install:
 	@ ${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>
+
+.include <bsd.port.mk>
diff --git a/biology/t_coffee/distinfo b/biology/t_coffee/distinfo
index 0da98a2be8e8..5589c4f91de5 100644
--- a/biology/t_coffee/distinfo
+++ b/biology/t_coffee/distinfo
@@ -1,2 +1,2 @@
-MD5 (T-COFFEE_distribution.tar.gz) = a947c75871f56e83ccc1e8444495330a
-SIZE (T-COFFEE_distribution.tar.gz) = 1368921
+MD5 (T-COFFEE_distribution_Version_2.03.tar.gz) = a86e2d83c17058b03be0170566d634f0
+SIZE (T-COFFEE_distribution_Version_2.03.tar.gz) = 864853
diff --git a/biology/t_coffee/files/patch-lalign-makefile b/biology/t_coffee/files/patch-lalign-makefile
deleted file mode 100644
index 4128d3cd6b0f..000000000000
--- a/biology/t_coffee/files/patch-lalign-makefile
+++ /dev/null
@@ -1,37 +0,0 @@
---- 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
deleted file mode 100644
index 58e654ff65fd..000000000000
--- a/biology/t_coffee/files/patch-t_coffee_source-makefile
+++ /dev/null
@@ -1,10 +0,0 @@
---- 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-descr b/biology/t_coffee/pkg-descr
index 304a8fc9eb80..ff1051aeb958 100644
--- a/biology/t_coffee/pkg-descr
+++ b/biology/t_coffee/pkg-descr
@@ -4,6 +4,10 @@ From the website:
   (Proteins or DNA), T-Coffee generates a multiple sequence alignment.
 
   Related publications:
+  - 3DCoffee: Combining Protein Sequences and Structures within Multiple
+    Sequence Alignments.
+    O. O'Sullivan, K Suhre, C. Abergel, D.G. Higgins, C. Notredame.
+    Journal of Molecular Biology, Vol 340, pp385-395, 2004
   - T-Coffee: A novel method for multiple sequence alignments.  C.Notredame,
     D. Higgins, J. Heringa, Journal of Molecular Biology,Vol 302,
     pp205-217,2000
diff --git a/biology/t_coffee/pkg-message b/biology/t_coffee/pkg-message
deleted file mode 100644
index 780b03c483ad..000000000000
--- a/biology/t_coffee/pkg-message
+++ /dev/null
@@ -1,10 +0,0 @@
---------------------------------------------------------------------------
-
-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
index 1100b4a356bb..d719ed2fdec2 100644
--- a/biology/t_coffee/pkg-plist
+++ b/biology/t_coffee/pkg-plist
@@ -1,305 +1,161 @@
+bin/t_coffee
+bin/msf_aln2fasta_aln.pl
+bin/blast_aln2fasta_aln.pl
+bin/fasta_aln2fasta_aln_unique_name.pl
+bin/extract_from_pdb
+bin/fugue_client
+bin/t_coffee_dpa
+bin/t_coffee_dpa2
+bin/mocca
 %%PORTDOCS%%%%DOCSDIR%%/README4T-COFFEE
 %%PORTDOCS%%%%DOCSDIR%%/t_coffee.pdf
 %%PORTDOCS%%%%DOCSDIR%%/t_coffee_doc.doc
-%%PORTDOCS%%%%DOCSDIR%%/t_coffee_doc.html
 %%PORTDOCS%%%%DOCSDIR%%/t_coffee_doc.pdf
-%%PORTDOCS%%%%DOCSDIR%%/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
-%%PORTDOCS%%share/examples/t_coffee/tc_aln/1aym3_ref1.t_coffee_aln10
-%%PORTDOCS%%share/examples/t_coffee/tc_aln/1bbt3_ref1.t_coffee_aln10
-%%PORTDOCS%%share/examples/t_coffee/tc_aln/1bgl_ref1.t_coffee_aln10
-%%PORTDOCS%%share/examples/t_coffee/tc_aln/1ckaA_ref4.t_coffee_aln10
-%%PORTDOCS%%share/examples/t_coffee/tc_aln/1cpt_ref1.t_coffee_aln10
-%%PORTDOCS%%share/examples/t_coffee/tc_aln/1cpt_ref2.t_coffee_aln10
-%%PORTDOCS%%share/examples/t_coffee/tc_aln/1csp_ref1.t_coffee_aln10
-%%PORTDOCS%%share/examples/t_coffee/tc_aln/1csp_ref4.t_coffee_aln10
-%%PORTDOCS%%share/examples/t_coffee/tc_aln/1csy_ref1.t_coffee_aln10
-%%PORTDOCS%%share/examples/t_coffee/tc_aln/1csy_ref2.t_coffee_aln10
-%%PORTDOCS%%share/examples/t_coffee/tc_aln/1dlc_ref1.t_coffee_aln10
-%%PORTDOCS%%share/examples/t_coffee/tc_aln/1dox_ref1.t_coffee_aln10
-%%PORTDOCS%%share/examples/t_coffee/tc_aln/1eft_ref1.t_coffee_aln10
-%%PORTDOCS%%share/examples/t_coffee/tc_aln/1eft_ref5.t_coffee_aln10
-%%PORTDOCS%%share/examples/t_coffee/tc_aln/1ezm_ref1.t_coffee_aln10
-%%PORTDOCS%%share/examples/t_coffee/tc_aln/1fieA_ref1.t_coffee_aln10
-%%PORTDOCS%%share/examples/t_coffee/tc_aln/1fjlA_ref1.t_coffee_aln10
-%%PORTDOCS%%share/examples/t_coffee/tc_aln/1fkj_ref1.t_coffee_aln10
-%%PORTDOCS%%share/examples/t_coffee/tc_aln/1fmb_ref1.t_coffee_aln10
-%%PORTDOCS%%share/examples/t_coffee/tc_aln/1gdoA_ref1.t_coffee_aln10
-%%PORTDOCS%%share/examples/t_coffee/tc_aln/1gowA_ref1.t_coffee_aln10
-%%PORTDOCS%%share/examples/t_coffee/tc_aln/1gpb_ref1.t_coffee_aln10
-%%PORTDOCS%%share/examples/t_coffee/tc_aln/1gtr_ref1.t_coffee_aln10
-%%PORTDOCS%%share/examples/t_coffee/tc_aln/1havA_ref1.t_coffee_aln10
-%%PORTDOCS%%share/examples/t_coffee/tc_aln/1havA_ref2.t_coffee_aln10
-%%PORTDOCS%%share/examples/t_coffee/tc_aln/1hfh_ref1.t_coffee_aln10
-%%PORTDOCS%%share/examples/t_coffee/tc_aln/1hpi_ref1.t_coffee_aln10
-%%PORTDOCS%%share/examples/t_coffee/tc_aln/1idy_ref1.t_coffee_aln10
-%%PORTDOCS%%share/examples/t_coffee/tc_aln/1idy_ref2.t_coffee_aln10
-%%PORTDOCS%%share/examples/t_coffee/tc_aln/1idy_ref3.t_coffee_aln10
-%%PORTDOCS%%share/examples/t_coffee/tc_aln/1ivy_ref5.t_coffee_aln10
-%%PORTDOCS%%share/examples/t_coffee/tc_aln/1krn_ref1.t_coffee_aln10
-%%PORTDOCS%%share/examples/t_coffee/tc_aln/1lcf_ref1.t_coffee_aln10
-%%PORTDOCS%%share/examples/t_coffee/tc_aln/1ldg_ref1.t_coffee_aln10
-%%PORTDOCS%%share/examples/t_coffee/tc_aln/1led_ref1.t_coffee_aln10
-%%PORTDOCS%%share/examples/t_coffee/tc_aln/1lkl_ref4.t_coffee_aln10
-%%PORTDOCS%%share/examples/t_coffee/tc_aln/1lvl_ref1.t_coffee_aln10
-%%PORTDOCS%%share/examples/t_coffee/tc_aln/1lvl_ref2.t_coffee_aln10
-%%PORTDOCS%%share/examples/t_coffee/tc_aln/1mfa_ref4.t_coffee_aln10
-%%PORTDOCS%%share/examples/t_coffee/tc_aln/1mrj_ref1.t_coffee_aln10
-%%PORTDOCS%%share/examples/t_coffee/tc_aln/1pamA_ref1.t_coffee_aln10
-%%PORTDOCS%%share/examples/t_coffee/tc_aln/1pamA_ref2.t_coffee_aln10
-%%PORTDOCS%%share/examples/t_coffee/tc_aln/1pamA_ref3.t_coffee_aln10
-%%PORTDOCS%%share/examples/t_coffee/tc_aln/1ped_ref1.t_coffee_aln10
-%%PORTDOCS%%share/examples/t_coffee/tc_aln/1ped_ref2.t_coffee_aln10
-%%PORTDOCS%%share/examples/t_coffee/tc_aln/1ped_ref3.t_coffee_aln10
-%%PORTDOCS%%share/examples/t_coffee/tc_aln/1pfc_ref1.t_coffee_aln10
-%%PORTDOCS%%share/examples/t_coffee/tc_aln/1pfc_ref4.t_coffee_aln10
-%%PORTDOCS%%share/examples/t_coffee/tc_aln/1pgtA_ref1.t_coffee_aln10
-%%PORTDOCS%%share/examples/t_coffee/tc_aln/1pii_ref1.t_coffee_aln10
-%%PORTDOCS%%share/examples/t_coffee/tc_aln/1pkm_ref1.t_coffee_aln10
-%%PORTDOCS%%share/examples/t_coffee/tc_aln/1plc_ref1.t_coffee_aln10
-%%PORTDOCS%%share/examples/t_coffee/tc_aln/1ppn_ref1.t_coffee_aln10
-%%PORTDOCS%%share/examples/t_coffee/tc_aln/1pysA_ref1.t_coffee_aln10
-%%PORTDOCS%%share/examples/t_coffee/tc_aln/1qpg_ref5.t_coffee_aln10
-%%PORTDOCS%%share/examples/t_coffee/tc_aln/1r69.t_coffee_aln10
-%%PORTDOCS%%share/examples/t_coffee/tc_aln/1r69_ref1.t_coffee_aln10
-%%PORTDOCS%%share/examples/t_coffee/tc_aln/1r69_ref2.t_coffee_aln10
-%%PORTDOCS%%share/examples/t_coffee/tc_aln/1r69_ref3.t_coffee_aln10
-%%PORTDOCS%%share/examples/t_coffee/tc_aln/1rthA_ref1.t_coffee_aln10
-%%PORTDOCS%%share/examples/t_coffee/tc_aln/1sbp_ref1.t_coffee_aln10
-%%PORTDOCS%%share/examples/t_coffee/tc_aln/1sbp_ref2.t_coffee_aln10
-%%PORTDOCS%%share/examples/t_coffee/tc_aln/1sesA_ref1.t_coffee_aln10
-%%PORTDOCS%%share/examples/t_coffee/tc_aln/1taq_ref1.t_coffee_aln10
-%%PORTDOCS%%share/examples/t_coffee/tc_aln/1tgxA_ref1.t_coffee_aln10
-%%PORTDOCS%%share/examples/t_coffee/tc_aln/1tgxA_ref2.t_coffee_aln10
-%%PORTDOCS%%share/examples/t_coffee/tc_aln/1thm1_ref5.t_coffee_aln10
-%%PORTDOCS%%share/examples/t_coffee/tc_aln/1thm2_ref5.t_coffee_aln10
-%%PORTDOCS%%share/examples/t_coffee/tc_aln/1thm_ref1.t_coffee_aln10
-%%PORTDOCS%%share/examples/t_coffee/tc_aln/1tis_ref1.t_coffee_aln10
-%%PORTDOCS%%share/examples/t_coffee/tc_aln/1ton_ref1.t_coffee_aln10
-%%PORTDOCS%%share/examples/t_coffee/tc_aln/1tvxA_ref1.t_coffee_aln10
-%%PORTDOCS%%share/examples/t_coffee/tc_aln/1tvxA_ref2.t_coffee_aln10
-%%PORTDOCS%%share/examples/t_coffee/tc_aln/1ubi_ref1.t_coffee_aln10
-%%PORTDOCS%%share/examples/t_coffee/tc_aln/1ubi_ref2.t_coffee_aln10
-%%PORTDOCS%%share/examples/t_coffee/tc_aln/1ubi_ref3.t_coffee_aln10
-%%PORTDOCS%%share/examples/t_coffee/tc_aln/1uky_ref1.t_coffee_aln10
-%%PORTDOCS%%share/examples/t_coffee/tc_aln/1uky_ref2.t_coffee_aln10
-%%PORTDOCS%%share/examples/t_coffee/tc_aln/1uky_ref3.t_coffee_aln10
-%%PORTDOCS%%share/examples/t_coffee/tc_aln/1vln_ref4.t_coffee_aln10
-%%PORTDOCS%%share/examples/t_coffee/tc_aln/1wit_ref1.t_coffee_aln10
-%%PORTDOCS%%share/examples/t_coffee/tc_aln/1wit_ref2.t_coffee_aln10
-%%PORTDOCS%%share/examples/t_coffee/tc_aln/1wit_ref3.t_coffee_aln10
-%%PORTDOCS%%share/examples/t_coffee/tc_aln/1ycc_ref1.t_coffee_aln10
-%%PORTDOCS%%share/examples/t_coffee/tc_aln/1ycc_ref4.t_coffee_aln10
-%%PORTDOCS%%share/examples/t_coffee/tc_aln/1zin_ref1.t_coffee_aln10
-%%PORTDOCS%%share/examples/t_coffee/tc_aln/2ack_ref1.t_coffee_aln10
-%%PORTDOCS%%share/examples/t_coffee/tc_aln/2cba_ref1.t_coffee_aln10
-%%PORTDOCS%%share/examples/t_coffee/tc_aln/2cba_ref5.t_coffee_aln10
-%%PORTDOCS%%share/examples/t_coffee/tc_aln/2fxb_ref1.t_coffee_aln10
-%%PORTDOCS%%share/examples/t_coffee/tc_aln/2hsdA_ref1.t_coffee_aln10
-%%PORTDOCS%%share/examples/t_coffee/tc_aln/2hsdA_ref2.t_coffee_aln10
-%%PORTDOCS%%share/examples/t_coffee/tc_aln/2mhr_ref1.t_coffee_aln10
-%%PORTDOCS%%share/examples/t_coffee/tc_aln/2myr_ref1.t_coffee_aln10
-%%PORTDOCS%%share/examples/t_coffee/tc_aln/2myr_ref2.t_coffee_aln10
-%%PORTDOCS%%share/examples/t_coffee/tc_aln/2myr_ref3.t_coffee_aln10
-%%PORTDOCS%%share/examples/t_coffee/tc_aln/2pia_ref1.t_coffee_aln10
-%%PORTDOCS%%share/examples/t_coffee/tc_aln/2pia_ref2.t_coffee_aln10
-%%PORTDOCS%%share/examples/t_coffee/tc_aln/2pia_ref3.t_coffee_aln10
-%%PORTDOCS%%share/examples/t_coffee/tc_aln/2trx_ref1.t_coffee_aln10
-%%PORTDOCS%%share/examples/t_coffee/tc_aln/2trx_ref2.t_coffee_aln10
-%%PORTDOCS%%share/examples/t_coffee/tc_aln/3cyr_ref1.t_coffee_aln10
-%%PORTDOCS%%share/examples/t_coffee/tc_aln/3grs_ref1.t_coffee_aln10
-%%PORTDOCS%%share/examples/t_coffee/tc_aln/3grs_ref2.t_coffee_aln10
-%%PORTDOCS%%share/examples/t_coffee/tc_aln/3pmg_ref1.t_coffee_aln10
-%%PORTDOCS%%share/examples/t_coffee/tc_aln/451c_ref1.t_coffee_aln10
-%%PORTDOCS%%share/examples/t_coffee/tc_aln/4enl_ref1.t_coffee_aln10
-%%PORTDOCS%%share/examples/t_coffee/tc_aln/4enl_ref2.t_coffee_aln10
-%%PORTDOCS%%share/examples/t_coffee/tc_aln/4enl_ref3.t_coffee_aln10
-%%PORTDOCS%%share/examples/t_coffee/tc_aln/5ptp_ref1.t_coffee_aln10
-%%PORTDOCS%%share/examples/t_coffee/tc_aln/9rnt_ref1.t_coffee_aln10
-%%PORTDOCS%%share/examples/t_coffee/tc_aln/S51_ref5.t_coffee_aln10
-%%PORTDOCS%%share/examples/t_coffee/tc_aln/S52_ref5.t_coffee_aln10
-%%PORTDOCS%%share/examples/t_coffee/tc_aln/actin_ref1.t_coffee_aln10
-%%PORTDOCS%%share/examples/t_coffee/tc_aln/arp_ref1.t_coffee_aln10
-%%PORTDOCS%%share/examples/t_coffee/tc_aln/gal4_ref1.t_coffee_aln10
-%%PORTDOCS%%share/examples/t_coffee/tc_aln/glg_ref1.t_coffee_aln10
-%%PORTDOCS%%share/examples/t_coffee/tc_aln/kinase1_ref4.t_coffee_aln10
-%%PORTDOCS%%share/examples/t_coffee/tc_aln/kinase1_ref5.t_coffee_aln10
-%%PORTDOCS%%share/examples/t_coffee/tc_aln/kinase2_ref4.t_coffee_aln10
-%%PORTDOCS%%share/examples/t_coffee/tc_aln/kinase2_ref5.t_coffee_aln10
-%%PORTDOCS%%share/examples/t_coffee/tc_aln/kinase3_ref5.t_coffee_aln10
-%%PORTDOCS%%share/examples/t_coffee/tc_aln/kinase_ref1.t_coffee_aln10
-%%PORTDOCS%%share/examples/t_coffee/tc_aln/kinase_ref2.t_coffee_aln10
-%%PORTDOCS%%share/examples/t_coffee/tc_aln/kinase_ref3.t_coffee_aln10
-%%PORTDOCS%%share/examples/t_coffee/test/reference_test.aln
-%%PORTDOCS%%share/examples/t_coffee/test/test.pep
-%%PORTDOCS%%share/t_coffee/t_coffee.html
-%%PORTDOCS%%share/t_coffee/t_coffee4html.cgi
-%%PORTDOCS%%share/t_coffee/t_coffee_doc.html
-bin/extract_from_pdb
-bin/lalign2list
-bin/mocca
-bin/t_coffee
-%%PORTDOCS%%@dirrm share/t_coffee
-%%PORTDOCS%%@dirrm share/examples/t_coffee/test
-%%PORTDOCS%%@dirrm share/examples/t_coffee/tc_aln
-%%PORTDOCS%%@dirrm share/examples/t_coffee/seq
-%%PORTDOCS%%@dirrm share/examples/t_coffee
+%%EXAMPLESDIR%%/seq/1aab_ref1.pep
+%%EXAMPLESDIR%%/seq/1aboA_ref1.pep
+%%EXAMPLESDIR%%/seq/1aboA_ref2.pep
+%%EXAMPLESDIR%%/seq/1ac5_ref1.pep
+%%EXAMPLESDIR%%/seq/1ad2_ref1.pep
+%%EXAMPLESDIR%%/seq/1ad3_ref1.pep
+%%EXAMPLESDIR%%/seq/1adj_ref1.pep
+%%EXAMPLESDIR%%/seq/1ag8_ref4.pep
+%%EXAMPLESDIR%%/seq/1aho_ref1.pep
+%%EXAMPLESDIR%%/seq/1aisB_ref4.pep
+%%EXAMPLESDIR%%/seq/1ajsA_ref1.pep
+%%EXAMPLESDIR%%/seq/1ajsA_ref2.pep
+%%EXAMPLESDIR%%/seq/1ajsA_ref3.pep
+%%EXAMPLESDIR%%/seq/1amk_ref1.pep
+%%EXAMPLESDIR%%/seq/1ar1_ref4.pep
+%%EXAMPLESDIR%%/seq/1ar5A_ref1.pep
+%%EXAMPLESDIR%%/seq/1au7A_ref4.pep
+%%EXAMPLESDIR%%/seq/1aym3_ref1.pep
+%%EXAMPLESDIR%%/seq/1bbt3_ref1.pep
+%%EXAMPLESDIR%%/seq/1bgl_ref1.pep
+%%EXAMPLESDIR%%/seq/1ckaA_ref4.pep
+%%EXAMPLESDIR%%/seq/1cpt_ref1.pep
+%%EXAMPLESDIR%%/seq/1cpt_ref2.pep
+%%EXAMPLESDIR%%/seq/1csp_ref1.pep
+%%EXAMPLESDIR%%/seq/1csp_ref4.pep
+%%EXAMPLESDIR%%/seq/1csy_ref1.pep
+%%EXAMPLESDIR%%/seq/1csy_ref2.pep
+%%EXAMPLESDIR%%/seq/1dlc_ref1.pep
+%%EXAMPLESDIR%%/seq/1dox_ref1.pep
+%%EXAMPLESDIR%%/seq/1eft_ref1.pep
+%%EXAMPLESDIR%%/seq/1eft_ref5.pep
+%%EXAMPLESDIR%%/seq/1ezm_ref1.pep
+%%EXAMPLESDIR%%/seq/1fieA_ref1.pep
+%%EXAMPLESDIR%%/seq/1fjlA_ref1.pep
+%%EXAMPLESDIR%%/seq/1fkj_ref1.pep
+%%EXAMPLESDIR%%/seq/1fmb_ref1.pep
+%%EXAMPLESDIR%%/seq/1gdoA_ref1.pep
+%%EXAMPLESDIR%%/seq/1gowA_ref1.pep
+%%EXAMPLESDIR%%/seq/1gpb_ref1.pep
+%%EXAMPLESDIR%%/seq/1gtr_ref1.pep
+%%EXAMPLESDIR%%/seq/1havA_ref1.pep
+%%EXAMPLESDIR%%/seq/1havA_ref2.pep
+%%EXAMPLESDIR%%/seq/1hfh_ref1.pep
+%%EXAMPLESDIR%%/seq/1hpi_ref1.pep
+%%EXAMPLESDIR%%/seq/1idy_ref1.pep
+%%EXAMPLESDIR%%/seq/1idy_ref2.pep
+%%EXAMPLESDIR%%/seq/1idy_ref3.pep
+%%EXAMPLESDIR%%/seq/1ivy_ref5.pep
+%%EXAMPLESDIR%%/seq/1krn_ref1.pep
+%%EXAMPLESDIR%%/seq/1lcf_ref1.pep
+%%EXAMPLESDIR%%/seq/1ldg_ref1.pep
+%%EXAMPLESDIR%%/seq/1led_ref1.pep
+%%EXAMPLESDIR%%/seq/1lkl_ref4.pep
+%%EXAMPLESDIR%%/seq/1lvl_ref1.pep
+%%EXAMPLESDIR%%/seq/1lvl_ref2.pep
+%%EXAMPLESDIR%%/seq/1mfa_ref4.pep
+%%EXAMPLESDIR%%/seq/1mrj_ref1.pep
+%%EXAMPLESDIR%%/seq/1pamA_ref1.pep
+%%EXAMPLESDIR%%/seq/1pamA_ref2.pep
+%%EXAMPLESDIR%%/seq/1pamA_ref3.pep
+%%EXAMPLESDIR%%/seq/1ped_ref1.pep
+%%EXAMPLESDIR%%/seq/1ped_ref2.pep
+%%EXAMPLESDIR%%/seq/1ped_ref3.pep
+%%EXAMPLESDIR%%/seq/1pfc_ref1.pep
+%%EXAMPLESDIR%%/seq/1pfc_ref4.pep
+%%EXAMPLESDIR%%/seq/1pgtA_ref1.pep
+%%EXAMPLESDIR%%/seq/1pii_ref1.pep
+%%EXAMPLESDIR%%/seq/1pkm_ref1.pep
+%%EXAMPLESDIR%%/seq/1plc_ref1.pep
+%%EXAMPLESDIR%%/seq/1ppn_ref1.pep
+%%EXAMPLESDIR%%/seq/1pysA_ref1.pep
+%%EXAMPLESDIR%%/seq/1qpg_ref5.pep
+%%EXAMPLESDIR%%/seq/1r69.pep
+%%EXAMPLESDIR%%/seq/1r69_ref1.pep
+%%EXAMPLESDIR%%/seq/1r69_ref2.pep
+%%EXAMPLESDIR%%/seq/1r69_ref3.pep
+%%EXAMPLESDIR%%/seq/1rthA_ref1.pep
+%%EXAMPLESDIR%%/seq/1sbp_ref1.pep
+%%EXAMPLESDIR%%/seq/1sbp_ref2.pep
+%%EXAMPLESDIR%%/seq/1sesA_ref1.pep
+%%EXAMPLESDIR%%/seq/1taq_ref1.pep
+%%EXAMPLESDIR%%/seq/1tgxA_ref1.pep
+%%EXAMPLESDIR%%/seq/1tgxA_ref2.pep
+%%EXAMPLESDIR%%/seq/1thm1_ref5.pep
+%%EXAMPLESDIR%%/seq/1thm2_ref5.pep
+%%EXAMPLESDIR%%/seq/1thm_ref1.pep
+%%EXAMPLESDIR%%/seq/1tis_ref1.pep
+%%EXAMPLESDIR%%/seq/1ton_ref1.pep
+%%EXAMPLESDIR%%/seq/1tvxA_ref1.pep
+%%EXAMPLESDIR%%/seq/1tvxA_ref2.pep
+%%EXAMPLESDIR%%/seq/1ubi_ref1.pep
+%%EXAMPLESDIR%%/seq/1ubi_ref2.pep
+%%EXAMPLESDIR%%/seq/1ubi_ref3.pep
+%%EXAMPLESDIR%%/seq/1uky_ref1.pep
+%%EXAMPLESDIR%%/seq/1uky_ref2.pep
+%%EXAMPLESDIR%%/seq/1uky_ref3.pep
+%%EXAMPLESDIR%%/seq/1vln_ref4.pep
+%%EXAMPLESDIR%%/seq/1wit_ref1.pep
+%%EXAMPLESDIR%%/seq/1wit_ref2.pep
+%%EXAMPLESDIR%%/seq/1wit_ref3.pep
+%%EXAMPLESDIR%%/seq/1ycc_ref1.pep
+%%EXAMPLESDIR%%/seq/1ycc_ref4.pep
+%%EXAMPLESDIR%%/seq/1zin_ref1.pep
+%%EXAMPLESDIR%%/seq/2ack_ref1.pep
+%%EXAMPLESDIR%%/seq/2cba_ref1.pep
+%%EXAMPLESDIR%%/seq/2cba_ref5.pep
+%%EXAMPLESDIR%%/seq/2fxb_ref1.pep
+%%EXAMPLESDIR%%/seq/2hsdA_ref1.pep
+%%EXAMPLESDIR%%/seq/2hsdA_ref2.pep
+%%EXAMPLESDIR%%/seq/2mhr_ref1.pep
+%%EXAMPLESDIR%%/seq/2myr_ref1.pep
+%%EXAMPLESDIR%%/seq/2myr_ref2.pep
+%%EXAMPLESDIR%%/seq/2myr_ref3.pep
+%%EXAMPLESDIR%%/seq/2pia_ref1.pep
+%%EXAMPLESDIR%%/seq/2pia_ref2.pep
+%%EXAMPLESDIR%%/seq/2pia_ref3.pep
+%%EXAMPLESDIR%%/seq/2trx_ref1.pep
+%%EXAMPLESDIR%%/seq/2trx_ref2.pep
+%%EXAMPLESDIR%%/seq/3cyr_ref1.pep
+%%EXAMPLESDIR%%/seq/3grs_ref1.pep
+%%EXAMPLESDIR%%/seq/3grs_ref2.pep
+%%EXAMPLESDIR%%/seq/3pmg_ref1.pep
+%%EXAMPLESDIR%%/seq/451c_ref1.pep
+%%EXAMPLESDIR%%/seq/4enl_ref1.pep
+%%EXAMPLESDIR%%/seq/4enl_ref2.pep
+%%EXAMPLESDIR%%/seq/4enl_ref3.pep
+%%EXAMPLESDIR%%/seq/5ptp_ref1.pep
+%%EXAMPLESDIR%%/seq/9rnt_ref1.pep
+%%EXAMPLESDIR%%/seq/S51_ref5.pep
+%%EXAMPLESDIR%%/seq/S52_ref5.pep
+%%EXAMPLESDIR%%/seq/actin_ref1.pep
+%%EXAMPLESDIR%%/seq/arp_ref1.pep
+%%EXAMPLESDIR%%/seq/gal4_ref1.pep
+%%EXAMPLESDIR%%/seq/glg_ref1.pep
+%%EXAMPLESDIR%%/seq/kinase1_ref4.pep
+%%EXAMPLESDIR%%/seq/kinase1_ref5.pep
+%%EXAMPLESDIR%%/seq/kinase2_ref4.pep
+%%EXAMPLESDIR%%/seq/kinase2_ref5.pep
+%%EXAMPLESDIR%%/seq/kinase3_ref5.pep
+%%EXAMPLESDIR%%/seq/kinase_ref1.pep
+%%EXAMPLESDIR%%/seq/kinase_ref2.pep
+%%EXAMPLESDIR%%/seq/kinase_ref3.pep
+%%EXAMPLESDIR%%/test/reference_test.aln
+%%EXAMPLESDIR%%/test/test.pep
 %%PORTDOCS%%@dirrm %%DOCSDIR%%
+@dirrm %%EXAMPLESDIR%%/seq
+@dirrm %%EXAMPLESDIR%%/test
+@dirrm %%EXAMPLESDIR%%