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/DESCR
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tcoffee/DESCR
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T-Coffee is a multiple sequence alignment package. Given a set of
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sequences (Proteins or DNA), T-Coffee generates a multiple sequence alignment.
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Multiple sequence alignment programs are to align a set of sequences
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previously gathered using other programs such as blast, fasta, etc.
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T-Coffee allows one to combine results obtained with several aligment
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methods. If one alignment is from ClustalW and second is from Dialigni,
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T-Coffee will combine all that information and produce a new multiple
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sequence having the best alignment from these methods.
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By default, T-Coffee will compare all your sequences two by two,
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producing a global alignment and a series of local alignments (using lalign).
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The program will then combine all these alignments into amultiple alignment.
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tcoffee/MESSAGE
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tcoffee/MESSAGE
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===========================================================================
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$NetBSD: MESSAGE,v 1.1.1.1 2004/11/29 18:05:21 daprice Exp $
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After Installing T-COFFEE, the environment variable CLUSTALW_4_TCOFFEE
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must be set to:
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${PREFIX}/bin
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===========================================================================
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tcoffee/Makefile
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tcoffee/Makefile
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# $NetBSD: Makefile,v 1.1.1.1 2004/11/29 18:05:21 daprice Exp $
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#
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DISTNAME= T-COFFEE_distribution
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PKGNAME= t-coffee-1.37
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WRKSRC= ${WRKDIR}/T-COFFEE_distribution_Version_1.37/t_coffee_source
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CATEGORIES= biology
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MASTER_SITES= http://igs-server.cnrs-mrs.fr/~cnotred/Packages/
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MAINTAINER= dprice@cs.nmsu.edu
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HOMEPAGE= http://igs-server.cnrs-mrs.fr/~cnotred/Packages/
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COMMENT= Multiple Sequence Alignment Package
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DEPENDS+= clustalw-1.8:../../biology/clustalw
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MESSAGE_SUBST+= PREFIX=${PREFIX}
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MAKEFILE= makefile
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USE_BUILDLINK3= yes
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do-install:
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${INSTALL_DATA_DIR} ${PREFIX}/share/doc/html/tcoffee
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.for HTML in t_coffee.html t_coffee4html.cgi t_coffee_doc.html
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${INSTALL_DATA} ${WRKSRC}/../html/${HTML} ${PREFIX}/share/doc/html/tcoffee
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.endfor
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${INSTALL_PROGRAM} ${WRKSRC}/../bin/t_coffee ${PREFIX}/bin
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${INSTALL_DATA_DIR} ${PREFIX}/share/doc/tcoffee
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.for DOC in README4T-COFFEE t_coffee_doc.doc t_coffee_doc.pdf \
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t_coffee.pdf t_coffee_doc.html t_coffee_doc.ps
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${INSTALL_DATA} ${WRKSRC}/../doc/${DOC} ${PREFIX}/share/doc/tcoffee
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.endfor
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.include "../../mk/bsd.pkg.mk"
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tcoffee/PLIST
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tcoffee/PLIST
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@comment $NetBSD: PLIST,v 1.1.1.1 2004/11/29 18:05:21 daprice Exp $
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bin/t_coffee
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share/doc/html/tcoffee/t_coffee.html
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share/doc/html/tcoffee/t_coffee4html.cgi
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share/doc/html/tcoffee/t_coffee_doc.html
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share/doc/tcoffee/README4T-COFFEE
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share/doc/tcoffee/t_coffee.pdf
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share/doc/tcoffee/t_coffee_doc.doc
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share/doc/tcoffee/t_coffee_doc.html
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share/doc/tcoffee/t_coffee_doc.pdf
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share/doc/tcoffee/t_coffee_doc.ps
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@dirrm share/doc/tcoffee
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@dirrm share/doc/html/tcoffee
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4
tcoffee/distinfo
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tcoffee/distinfo
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$NetBSD: distinfo,v 1.1.1.1 2004/11/29 18:05:21 daprice Exp $
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SHA1 (T-COFFEE_distribution.tar.gz) = f1ab1c5db2358befa1f08724362ca5c7bf0ca9ba
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Size (T-COFFEE_distribution.tar.gz) = 1368921 bytes
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