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* add avida 1.6.0ijliao2002-04-201-0/+1
| | | | | | | Avida is an auto-adaptive genetic system designed for ALife research PR: 37268 Submitted by: Jeremy Karlson <karlj000@unbc.ca>
* Swiss-PdbViewer is an application that provides a user friendly interfacedinoex2002-04-031-0/+1
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | 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
* Add crimap 2.4, a tool for the creation of multilocus linkage maps.wjv2002-03-271-0/+1
| | | | | PR: 35198 Submitted by: Tony Maher <tonym@biolateral.com.au>
* Add tRNAscan-SE 1.21, an improved tool for transfer RNA detection.wjv2002-03-271-0/+1
| | | | | PR: 33853 Submitted by: chuynh@biolateral.com.au
* Add t_coffee 1.37, a multiple DNA or protein sequence alignment package.wjv2002-01-251-0/+1
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* Initial import of artemis 4.0kevlo2001-12-221-0/+1
| | | | | | | Artemis is a DNA sequence viewer and annotation tool. PR: 32914 Submitted by: Camson <chuynh@biolateral.com.au>
* Add gff2ps 0.97b, converts gff-formated genomic data-sets topetef2001-12-191-0/+1
| | | | | | | PostScript. PR: 32920 Submitted by: Camson Huynh <chuynh@biolateral.com.au>
* Add dna-qc 1993.07.26, a quality control algorithm for DNApetef2001-12-191-0/+1
| | | | | | | sequencing projects. PR: 32998 Submitted by: Tony Maher <tonym@biolateral.com.au>
* Add ruby-bio (BioRuby), an integrated environment for Bioinformaticsknu2001-10-241-0/+1
| | | | written in Ruby.
* Add nclever 4.0, a character-based version of NCBI's Entrez program.wjv2001-09-261-0/+1
| | | | | PR: 30783 Submitted by: Tony Maher <tonym@biolateral.com.au>
* Add seqio 1.2.2, a set of C functions which can read/writewjv2001-08-221-0/+1
| | | | | | | biological sequence files. PR: 29922 Submitted by: Tony Maher <tonym@biolateral.com.au>
* Add treeviewx 0.1.1, a phylogenetic tree viewer.wjv2001-08-171-0/+1
| | | | | PR: 29770 Submitted by: Tony Maher <tonym@biolateral.com.au>
* Add p5-bioperl-devel 0.9.0,wjv2001-08-141-0/+1
| | | | | a collection of Perl modules for bioinformatics (developer's release).
* Add lamarc 2001.08.06,wjv2001-08-071-0/+1
| | | | | a package of programs for computing population parameters.
* Add recombine 1.40, a program to fit population models across sites.wjv2001-08-061-0/+1
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* Add fluctuate 1.30, a program to fit population models.wjv2001-08-061-0/+1
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* Add coalesce 1.50, a program to fit population models.wjv2001-08-061-0/+1
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* Add migrate 1.2,wjv2001-08-061-0/+1
| | | | | a program to estimate population sizes and migration rates.
* Add grappa 1.0.2, Genome Rearrangements Analysis and Phylogenywjv2001-07-041-0/+1
| | | | | | | Software. PR: 28541 Submitted by: dbader@eece.unm.edu
* reimport biology/genpakijliao2001-02-281-0/+1
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* module name conflict with print/gp, so remove it and I'll reimport it againijliao2001-02-281-1/+0
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* add gpijliao2001-02-281-0/+1
| | | | GP is a set of small utilities to manipulate DNA sequences
* - New port: biology/fasta3, which comprises the FASTA3 suite of DNA andjeh2001-02-121-0/+1
| | | | | | | | | protein sequence search programs - FASTA3 updates only some of the elements of FASTA2, which is why I have submitted ports of both versions (as biology/fasta and biology/fasta3) PR: 24716 Submitted by: Johann Visagie <johann@egenetics.com>
* New port: biology/fasta, the FASTA2 suite of DNA and protein sequencejeh2001-02-121-0/+1
| | | | | | | search tools PR: 24715 Submitted by: Johann Visagie <johann@egenetics.com>
* add gaussian98, an ab-initio molecular orbital calculation program.sf2001-02-111-0/+1
| | | | | PR: 23577 Submitted by: NAKATA, Maho <chat95@mbox.kyoto-inet.or.jp>
* New Port: biology/ncbi-toolkitjeh2000-10-291-0/+1
| | | | | | | National Center for Biotechnology Information (NCBI) Development Toolkit. PR: 22388 Submitted by: Tony Maher <tony.maher@ebioinformatics.com>
* Initial import of fastDNAml Version 1.2.2jeh2000-10-121-0/+1
| | | | | | | The faster variant of DNAML, makes phylogenetic trees using maximum likelihood PR: 21931 Submitted by: Motomichi Matsuzaki <mzaki@e-mail.ne.jp>
* Initial import of biology/biojavajeh2000-10-101-0/+1
| | | | | PR: 21678 Submitted by: Brad Chapman <chapmanb@arches.uga.edu>
* This is nab (nucleic acid builder), a language for macromoleculesjeh2000-10-101-0/+1
| | | | | PR: 21585 Submitted by: M. L. Dodson <bdodson@scms.utmb.EDU>
* Add emboss, the European Molecular Biology Open Software Suitenbm2000-08-011-0/+1
| | | | | PR: ports/20317 Submitted by: Johann Visagie <johann@egenetics.com>
* Add py-biopython, is a collection of Python packages and modules creatednbm2000-07-311-0/+1
| | | | | | | | by the Biopython Project, intended to provide the basis for building bioinformatics applications in the Python language. PR: ports/20260 Submitted by: Johann Visagie <johann@egenetics.com>
* Add BioPerl, a collection of Perl5 mods for bioinformatics/genomicsnbm2000-07-281-0/+1
| | | | | PR: ports/20252 Submitted by: Johann Visagie <johann@egenetics.com>
* Add p5-AcePerl, a perl interface to the ACEDB genome database systemnbm2000-07-281-0/+1
| | | | | PR: ports/20223 Submitted by: Johann Visagie <johann@egenetics.com>
* Add sim4, an implementation of the sim4 algorithm for aligning expressednbm2000-07-271-0/+1
| | | | | | | DNA with genomic sequences PR: ports/20219 Submitted by: Johann Visagie <johann@egenetics.com>
* Add xdrawchem 0.82 - a program for drawing moleculesalex2000-07-191-0/+1
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* Activating the chemeq, clustalw, paml, and phylip ports.steve2000-07-101-0/+4
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* Added gperiodic and xmolwttaoka1999-09-071-0/+2
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* Change Id->FreeBSD.obrien1999-08-251-1/+1
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* Added deft and ortep3taoka1999-05-191-1/+3
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* Add platon and moldentaoka1999-05-071-1/+3
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* Add mopac and psi88 (Move mopac and psi88 from misc to biology)taoka1999-05-061-1/+3
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* Activate tinker.jkoshy1998-11-171-1/+2
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* Turn on hmmer.steve1998-07-131-1/+2
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* Activate povchem.vanilla1998-03-161-1/+2
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* Activate kinemagejseger1998-01-301-1/+2
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* Activate seaview.vanilla1997-12-221-1/+2
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* Activate babel.vanilla1997-12-221-1/+2
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* Activate rasmol.vanilla1997-12-161-2/+2
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* The new ports category "biology" starts here today. No Darwinasami1997-12-131-0/+6
jokes please!
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