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T-Coffee is a multiple sequence alignment package. Given a set of sequences (Proteins or DNA), T-Coffee generates a multiple sequence alignment. Multiple sequence alignment programs are to align a set of sequences previously gathered using other programs such as blast, fasta, etc. T-Coffee allows one to combine results obtained with several aligment methods. If one alignment is from ClustalW and second is from Dialigni, T-Coffee will combine all that information and produce a new multiple sequence having the best alignment from these methods. By default, T-Coffee will compare all your sequences two by two, producing a global alignment and a series of local alignments (using lalign). The program will then combine all these alignments into amultiple alignment.

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David 2004-11-29 18:05:21 +00:00 committed by Thomas Klausner
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T-Coffee is a multiple sequence alignment package. Given a set of
sequences (Proteins or DNA), T-Coffee generates a multiple sequence alignment.
Multiple sequence alignment programs are to align a set of sequences
previously gathered using other programs such as blast, fasta, etc.
T-Coffee allows one to combine results obtained with several aligment
methods. If one alignment is from ClustalW and second is from Dialigni,
T-Coffee will combine all that information and produce a new multiple
sequence having the best alignment from these methods.
By default, T-Coffee will compare all your sequences two by two,
producing a global alignment and a series of local alignments (using lalign).
The program will then combine all these alignments into amultiple alignment.

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tcoffee/MESSAGE Normal file
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===========================================================================
$NetBSD: MESSAGE,v 1.1.1.1 2004/11/29 18:05:21 daprice Exp $
After Installing T-COFFEE, the environment variable CLUSTALW_4_TCOFFEE
must be set to:
${PREFIX}/bin
===========================================================================

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# $NetBSD: Makefile,v 1.1.1.1 2004/11/29 18:05:21 daprice Exp $
#
DISTNAME= T-COFFEE_distribution
PKGNAME= t-coffee-1.37
WRKSRC= ${WRKDIR}/T-COFFEE_distribution_Version_1.37/t_coffee_source
CATEGORIES= biology
MASTER_SITES= http://igs-server.cnrs-mrs.fr/~cnotred/Packages/
MAINTAINER= dprice@cs.nmsu.edu
HOMEPAGE= http://igs-server.cnrs-mrs.fr/~cnotred/Packages/
COMMENT= Multiple Sequence Alignment Package
DEPENDS+= clustalw-1.8:../../biology/clustalw
MESSAGE_SUBST+= PREFIX=${PREFIX}
MAKEFILE= makefile
USE_BUILDLINK3= yes
do-install:
${INSTALL_DATA_DIR} ${PREFIX}/share/doc/html/tcoffee
.for HTML in t_coffee.html t_coffee4html.cgi t_coffee_doc.html
${INSTALL_DATA} ${WRKSRC}/../html/${HTML} ${PREFIX}/share/doc/html/tcoffee
.endfor
${INSTALL_PROGRAM} ${WRKSRC}/../bin/t_coffee ${PREFIX}/bin
${INSTALL_DATA_DIR} ${PREFIX}/share/doc/tcoffee
.for DOC in README4T-COFFEE t_coffee_doc.doc t_coffee_doc.pdf \
t_coffee.pdf t_coffee_doc.html t_coffee_doc.ps
${INSTALL_DATA} ${WRKSRC}/../doc/${DOC} ${PREFIX}/share/doc/tcoffee
.endfor
.include "../../mk/bsd.pkg.mk"

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@comment $NetBSD: PLIST,v 1.1.1.1 2004/11/29 18:05:21 daprice Exp $
bin/t_coffee
share/doc/html/tcoffee/t_coffee.html
share/doc/html/tcoffee/t_coffee4html.cgi
share/doc/html/tcoffee/t_coffee_doc.html
share/doc/tcoffee/README4T-COFFEE
share/doc/tcoffee/t_coffee.pdf
share/doc/tcoffee/t_coffee_doc.doc
share/doc/tcoffee/t_coffee_doc.html
share/doc/tcoffee/t_coffee_doc.pdf
share/doc/tcoffee/t_coffee_doc.ps
@dirrm share/doc/tcoffee
@dirrm share/doc/html/tcoffee

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$NetBSD: distinfo,v 1.1.1.1 2004/11/29 18:05:21 daprice Exp $
SHA1 (T-COFFEE_distribution.tar.gz) = f1ab1c5db2358befa1f08724362ca5c7bf0ca9ba
Size (T-COFFEE_distribution.tar.gz) = 1368921 bytes