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* Note distribution term.sada2002-05-271-8/+6
| | | | Requested by: maintainer
* Back my last commit out.sada2002-05-232-2/+2
| | | | | | We couldn't update distinfo without inspecting distfile's changes. PR: ports/37476 Suggested by: kris
* distfile has silently changed,sada2002-05-182-1/+2
| | | | | | so md5 has to be rewritten. PR: ports/37476 Submitted by: maintainer
* BROKEN: Checksum is incorrectkris2002-05-181-0/+2
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* BROKEN: incorrect checksumskris2002-05-171-0/+2
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* Update to sim4-2002.03.03 to unbreak build.kris2002-05-042-3/+3
| | | | Noticed by: bento
* upgrade to V110-1ijliao2002-04-212-4/+3
| | | | | | | | build with newer bison remove BROKEN PR: 37313 Submitted by: maintainer
* add avida 1.6.0ijliao2002-04-2011-0/+146
| | | | | | | Avida is an auto-adaptive genetic system designed for ALife research PR: 37268 Submitted by: Jeremy Karlson <karlj000@unbc.ca>
* Update to 0.3.6.knu2002-04-102-4/+3
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* Swiss-PdbViewer is an application that provides a user friendly interfacedinoex2002-04-028-0/+388
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | allowing to analyse several proteins at the same time. The proteins can be superimposed in order to deduce structural alignments and compare their active sites or any other relevant parts. Amino acid mutations, H-bonds, angles and distances between atoms are easy to obtain thanks to the intuitive graphic and menu interface. Moreover, Swiss-PdbViewer is tightly linked to Swiss-Model, an automated homology modelling server developped at Glaxo Welcome Experimental Research in Geneva. Working with these two programs greatly reduces the amount of work necessary to generate models, as it is possible to thread a protein primary sequence onto a 3D template and get an immediate feedback of how well the threaded protein will be accepted by the reference structure before submitting a request to build missing loops and refine sidechain packing. Swiss-PdbViewer can also read electron density maps, and provides various tools to build into the density. In addition, various modelling tools are integrated and command files for popular energy minimisation packages can be generated. Finally, as a special bonus, POV-Ray scenes can be generated from the current view in order to make stunning ray-traced quality images. WWW: http://www.expasy.ch/spdbv/ PR: 33902 Submitted by: chuynh@biolateral.com.au
* Remove #include <malloc.h>kris2002-03-311-0/+4
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* change master siteijliao2002-03-293-10/+32
| | | | | | | add mpich support PR: 36468 Submitted by: maintainer
* Respect CFLAGS/CC.petef2002-03-281-0/+21
| | | | | | PR: 36395 Submitted by: maintainer Reported by: bento
* Add crimap 2.4, a tool for the creation of multilocus linkage maps.wjv2002-03-276-0/+59
| | | | | PR: 35198 Submitted by: Tony Maher <tonym@biolateral.com.au>
* Add tRNAscan-SE 1.21, an improved tool for transfer RNA detection.wjv2002-03-277-0/+102
| | | | | PR: 33853 Submitted by: chuynh@biolateral.com.au
* - Add a new patchwjv2002-03-272-1/+11
| | | | | | | - Bump $PORTREVISION PR: 36206 Submitted by: David A. Bader <dbader@eece.unm.edu> (MAINTAINER)
* Add USE_SUBMAKE, where it might be necessary.sobomax2002-03-251-0/+1
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* BROKEN: Does not buildkris2002-03-251-0/+2
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* - Fix certain mistakes in FreeBSD patcheswjv2002-03-228-70/+320
| | | | | | | | | - Bump PORTREVISION - Poroblem originally reported by Fernan Aguero <fernan@iib.unsam.edu.ar> on FreeBSD-bio list PR: 36169 Submitted by: David A. Bader <dbader@eece.unm.edu> (MAINTAINER)
* Update to 0.3.5.knu2002-03-123-3/+13
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* Fix WWW.dannyboy2002-03-081-1/+1
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* Update to 2001.12.20pat2002-02-226-18/+88
| | | | | PR: 35203 Submitted by: maintainer
* Pass maintainership to submitter and add a backup master site.petef2002-02-201-2/+3
| | | | | PR: 35043 Submitted by: Christian Brueffer <chris@unixpages.org>
* - Install documentationpat2002-02-134-6/+19
| | | | | | | - Update WWW: PR: 34889 Submitted by: maintainer
* Use ${ECHO_CMD} instead of ${ECHO} where you mean the echo command;knu2002-01-291-4/+4
| | | | | | | | the ECHO macro is set to "echo" by default, but it is set to "true" if make(1) is invoked with the -s option while ECHO_CMD is always set to the echo command. Use command macros where appropriate.
* Add t_coffee 1.37, a multiple DNA or protein sequence alignment package.wjv2002-01-259-0/+438
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* - Update to version of 2001-12-30wjv2002-01-252-2/+2
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* - Update to version 1.82wjv2002-01-254-13/+28
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* - Update to version 0.7.2, somewhat overdue. :-)wjv2002-01-252-27/+53
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* o update to 3.7.sf2002-01-232-34/+7
| | | | | | | | | differences from the PR: - this port requires Xlib so add USE_XLIB. - remove unnecessary PORTREVISION. PR: 34196 Submitted by: maintainer
* o update to 0.7.sf2002-01-232-2/+2
| | | | | PR: 34197 Submitted by: maintainer
* update to 1.3.3.sf2002-01-222-2/+2
| | | | | PR: 34180 Submitted by: KATO Tsuguru <tkato@prontomail.com>
* - Update to version 1.00a4wjv2002-01-223-10/+261
| | | | | PR: 33719 Submitted by: Hye-Shik Chang <perky@fallin.lv>
* Update to 0.99.7. Use new DATADIR macro. Install documentation,trevor2002-01-204-24/+55
| | | | including examples. Add warning.
* Upgrade tinker to the latest revisionijliao2002-01-195-64/+101
| | | | | PR: 33425 Submitted by: maintainer
* - Update to version 2.2.0wjv2002-01-183-15/+335
| | | | | | | | | - Update included EMBASSY package EMNU - Fix a long-standing bug in Makefile that would preclude PKGMESSAGE from being generated properly - Consider this an interim update merely to track the latest version - more work is required to activate the newly included "Jemboss" Java GUI interface
* Update to 0.2.petef2001-12-294-19/+8
| | | | | PR: 33218 Submitted by: maintainer
* Initial import of artemis 4.0kevlo2001-12-226-0/+1529
| | | | | | | Artemis is a DNA sequence viewer and annotation tool. PR: 32914 Submitted by: Camson <chuynh@biolateral.com.au>
* Update to 0.3.3.knu2001-12-213-2/+3
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* Add gff2ps 0.97b, converts gff-formated genomic data-sets topetef2001-12-196-0/+42
| | | | | | | PostScript. PR: 32920 Submitted by: Camson Huynh <chuynh@biolateral.com.au>
* Add dna-qc 1993.07.26, a quality control algorithm for DNApetef2001-12-197-0/+94
| | | | | | | sequencing projects. PR: 32998 Submitted by: Tony Maher <tonym@biolateral.com.au>
* Update to version 2001.10.12.steve2001-12-162-2/+2
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* fix pkg-plistijliao2001-12-081-0/+1
| | | | | PR: 32609 Submitted by: Ports Fury
* * Replace pkg-message about setting BABEL_DIR with a wrapper scriptnaddy2001-12-028-26/+55
| | | | | | | | that does. * Remove misleading full path name from usage message. * Improve fgets() usage. * Add converters category. * Improve pkg-comment and pkg-descr.
* - update to 1.3.2petef2001-11-282-7/+4
| | | | | | | - use DOCSDIR PR: 32305 Submitted by: KATO Tsuguru <tkato@prontomail.com>
* Update to 0.3.2.knu2001-11-283-4/+21
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* Style police: WWW tags should either end in a file/script or TRAILING /; Fix ↵lioux2001-11-201-1/+1
| | | | the later case
* Style police: WWW tags should either end in a file/script or TRAILING /; Fix ↵lioux2001-11-202-2/+2
| | | | the later case
* chase checksum for repacked distfile almost an year ago.sf2001-11-063-2/+3
| | | | | | | | | Maintainer does not have previous distfile. As the distfile for this port is not distributable, it is OK to me to change distinfo now. PR: 31010 Submitted by: maintainer
* Add ruby-bio (BioRuby), an integrated environment for Bioinformaticsknu2001-10-246-0/+91
| | | | written in Ruby.
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