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- Update to 2.03

Browse Source 
- Pass maintainership to submitter

PR:		ports/74332
Submitted by:	Fernan Aguero <fernan(at)iib.unsam.edu.ar>
This commit is contained in:
Sergey Matveychuk 2004-11-25 23:03:54 +00:00
parent 5275953004
commit d667344504
Notes: svn2git 2021-03-31 03:12:20 +00:00 
svn path=/head/; revision=122437
7 changed files with 175 additions and 384 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

38
biology/t_coffee/Makefile
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@ -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
MAKE_ENV= MV=${MV} USER_BIN=${PREFIX}/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>
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>

4
biology/t_coffee/distinfo
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@ -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

37
biology/t_coffee/files/patch-lalign-makefile
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@ -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

10
biology/t_coffee/files/patch-t_coffee_source-makefile
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@ -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

4
biology/t_coffee/pkg-descr
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@ -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

10
biology/t_coffee/pkg-message
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@ -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.
--------------------------------------------------------------------------

456
biology/t_coffee/pkg-plist
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@ -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
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%%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
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%%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
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%%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
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%%PORTDOCS%%share/examples/t_coffee/seq/gal4_ref1.pep
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%%PORTDOCS%%share/examples/t_coffee/seq/kinase1_ref4.pep
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%%PORTDOCS%%share/examples/t_coffee/seq/kinase2_ref4.pep
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%%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
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%%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
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%%PORTDOCS%%share/examples/t_coffee/tc_aln/1aym3_ref1.t_coffee_aln10
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%%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
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bin/extract_from_pdb
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