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* [new port] biology/embassySergey Matveychuk2004-11-261-0/+1
| | | | | | | | PR: ports/74330 Submitted by: Fernan Aguero <fernan(at)iib.unsam.edu.ar> Notes: svn path=/head/; revision=122510
* Add blast, a powerful software package for gene and protein identification,Pav Lucistnik2004-11-111-0/+1
| | | | | | | | | | | using sensitive, selective and rapid similarity searches of protein and nucleotide sequence databases. PR: ports/69636 Submitted by: Fernan Aguero <fernan@iib.unsam.edu.ar> Notes: svn path=/head/; revision=121414
* Add ariadne 1.3, programs to compare protein sequences andKirill Ponomarev2004-06-221-0/+1
| | | | | | | | | | profiles, using the Smith-Waterman algorithm. PR: ports/67811 Submitted by: Fernan Aguero <fernan@iib.unsam.edu.ar> Notes: svn path=/head/; revision=111985
* Remove category pkg/COMMENT files in favour of a COMMENT variable in theKris Kennaway2004-04-021-0/+2
| | | | | | | | | | category makefile. Submitted by: Matthew Seaman <m.seaman@infracaninophile.co.uk> PR: 59651 Notes: svn path=/head/; revision=105948
* new port:biology/lsysexpEdwin Groothuis2003-09-031-0/+1
| | | | | | | | | | | | | | | | | | | | | L-system Explorer is a program used for viewing and creating L-system fractals. The following features are supported: - Over 500 builtin L-systems, arranged into about 20 groups. - Ability to create and save custom L-systems and L-system groups. - Abilty to save images of L-systems (in PNG or JPEG format). - Multiple L-systems can be viewed at the same time. - Able to use custom colors and gradients. - Can also generate random gradients, or completely random colors. - Able to draw using lines, points, or a random combination of both. PR: iports/51400 Submitted by: David Yeske <dyeske@yahoo.com> Notes: svn path=/head/; revision=88397
* As announced on May 6, remove the broken p5-bioperl-devel port.Kris Kennaway2003-08-081-1/+0
| | | | Notes: svn path=/head/; revision=86539
* A new port garlic, free molecular viewer and editor, free molecularMaho Nakata2003-07-281-0/+1
| | | | | | | | visualization program, protein structure, DNA structure, PDB, molecular rendering, biological macromolecule. Notes: svn path=/head/; revision=85720
* Remove gaussian98Kris Kennaway2003-02-051-1/+0
| | | | | | | Pointy hat to: maho Notes: svn path=/head/; revision=74811
* New Port: biology/actEdwin Groothuis2003-01-161-0/+1
| | | | | | | | PR: ports/35753 Submitted by: Camson Huynh <chuynh@biolateral.com.au> Notes: svn path=/head/; revision=73258
* add treepuzzle 5.1Ying-Chieh Liao2002-11-201-0/+1
| | | | | | | | | | Maximum likelihood phylogeny reconstruction using quartets PR: 45241 Submitted by: Jan Lentfer <lentferj@neslonek.bio.tu-darmstadt.de> Notes: svn path=/head/; revision=70552
* Connect distribfold to build after moving it from misc categoryMario Sergio Fujikawa Ferreira2002-10-071-0/+1
| | | | | | | | | | Prompted by: kris, Adam Weinberger <adam@vectors.cx>, Fernan Aguero <fernan@iib.unsam.edu.ar>, others Notes: svn path=/head/; revision=67526
* add primer3 0.9Ying-Chieh Liao2002-09-171-0/+1
| | | | | | | | | | Primer3 helps to choose primers for PCR reactions PR: 35298 Submitted by: Tony Maher <tonym@biolateral.com.au> Notes: svn path=/head/; revision=66513
* Flip is used to find/translate orfs.Dirk Meyer2002-09-101-0/+1
| | | | | | | | | WWW: ftp://megasun.bch.umontreal.ca/pub/flip/ PR: 35332 Submitted by: tonym@biolateral.com.au Notes: svn path=/head/; revision=66055
* "Wise2 is package that is focused on comparing DNA sequences atDirk Meyer2002-09-101-0/+1
| | | | | | | | the level of its conceptual translation, regardless of sequencing error and introns." Notes: svn path=/head/; revision=66053
* New port L-Breeder version 1.0: Allows you to display and breedMario Sergio Fujikawa Ferreira2002-08-211-0/+1
| | | | | | | | | | L-system forms PR: 38725 Submitted by: David Yeske <dyeske@yahoo.com> Notes: svn path=/head/; revision=64720
* Add pymol 0.82, Free and Open-Source molecular modeling system.Hye-Shik Chang2002-08-131-0/+1
| | | | | | | | PR: 40694 Submitted by: Nakata Maho <chat95@mbox.kyoto-inet.or.jp> Notes: svn path=/head/; revision=64463
* add libgenome 0.5.0Ying-Chieh Liao2002-07-301-0/+1
| | | | | | | Toolkit for developing bioinformatic related software in C++ Notes: svn path=/head/; revision=63725
* add avida 1.6.0Ying-Chieh Liao2002-04-201-0/+1
| | | | | | | | | | Avida is an auto-adaptive genetic system designed for ALife research PR: 37268 Submitted by: Jeremy Karlson <karlj000@unbc.ca> Notes: svn path=/head/; revision=57919
* Swiss-PdbViewer is an application that provides a user friendly interfaceDirk Meyer2002-04-021-0/+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 Notes: svn path=/head/; revision=57214
* Add crimap 2.4, a tool for the creation of multilocus linkage maps.Johann Visagie2002-03-271-0/+1
| | | | | | | | PR: 35198 Submitted by: Tony Maher <tonym@biolateral.com.au> Notes: svn path=/head/; revision=56744
* Add tRNAscan-SE 1.21, an improved tool for transfer RNA detection.Johann Visagie2002-03-271-0/+1
| | | | | | | | PR: 33853 Submitted by: chuynh@biolateral.com.au Notes: svn path=/head/; revision=56741
* Add t_coffee 1.37, a multiple DNA or protein sequence alignment package.Johann Visagie2002-01-251-0/+1
| | | | Notes: svn path=/head/; revision=53719
* Initial import of artemis 4.0Kevin Lo2001-12-221-0/+1
| | | | | | | | | | Artemis is a DNA sequence viewer and annotation tool. PR: 32914 Submitted by: Camson <chuynh@biolateral.com.au> Notes: svn path=/head/; revision=51988
* Add gff2ps 0.97b, converts gff-formated genomic data-sets toPete Fritchman2001-12-191-0/+1
| | | | | | | | | | PostScript. PR: 32920 Submitted by: Camson Huynh <chuynh@biolateral.com.au> Notes: svn path=/head/; revision=51813
* Add dna-qc 1993.07.26, a quality control algorithm for DNAPete Fritchman2001-12-191-0/+1
| | | | | | | | | | sequencing projects. PR: 32998 Submitted by: Tony Maher <tonym@biolateral.com.au> Notes: svn path=/head/; revision=51777
* Add ruby-bio (BioRuby), an integrated environment for BioinformaticsAkinori MUSHA2001-10-241-0/+1
| | | | | | | written in Ruby. Notes: svn path=/head/; revision=49156
* Add nclever 4.0, a character-based version of NCBI's Entrez program.Johann Visagie2001-09-261-0/+1
| | | | | | | | PR: 30783 Submitted by: Tony Maher <tonym@biolateral.com.au> Notes: svn path=/head/; revision=48207
* Add seqio 1.2.2, a set of C functions which can read/writeJohann Visagie2001-08-221-0/+1
| | | | | | | | | | biological sequence files. PR: 29922 Submitted by: Tony Maher <tonym@biolateral.com.au> Notes: svn path=/head/; revision=46640
* Add treeviewx 0.1.1, a phylogenetic tree viewer.Johann Visagie2001-08-171-0/+1
| | | | | | | | PR: 29770 Submitted by: Tony Maher <tonym@biolateral.com.au> Notes: svn path=/head/; revision=46356
* Add p5-bioperl-devel 0.9.0,Johann Visagie2001-08-141-0/+1
| | | | | | | | a collection of Perl modules for bioinformatics (developer's release). Notes: svn path=/head/; revision=46228
* Add lamarc 2001.08.06,Johann Visagie2001-08-071-0/+1
| | | | | | | | a package of programs for computing population parameters. Notes: svn path=/head/; revision=45915
* Add recombine 1.40, a program to fit population models across sites.Johann Visagie2001-08-061-0/+1
| | | | Notes: svn path=/head/; revision=45886
* Add fluctuate 1.30, a program to fit population models.Johann Visagie2001-08-061-0/+1
| | | | Notes: svn path=/head/; revision=45885
* Add coalesce 1.50, a program to fit population models.Johann Visagie2001-08-061-0/+1
| | | | Notes: svn path=/head/; revision=45884
* Add migrate 1.2,Johann Visagie2001-08-061-0/+1
| | | | | | | | a program to estimate population sizes and migration rates. Notes: svn path=/head/; revision=45878
* Add grappa 1.0.2, Genome Rearrangements Analysis and PhylogenyJohann Visagie2001-07-041-0/+1
| | | | | | | | | | Software. PR: 28541 Submitted by: dbader@eece.unm.edu Notes: svn path=/head/; revision=44738
* reimport biology/genpakYing-Chieh Liao2001-02-281-0/+1
| | | | Notes: svn path=/head/; revision=38875
* module name conflict with print/gp, so remove it and I'll reimport it againYing-Chieh Liao2001-02-281-1/+0
| | | | Notes: svn path=/head/; revision=38874
* add gpYing-Chieh Liao2001-02-271-0/+1
| | | | | | | GP is a set of small utilities to manipulate DNA sequences Notes: svn path=/head/; revision=38854
* - New port: biology/fasta3, which comprises the FASTA3 suite of DNA andJames E. Housley2001-02-111-0/+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> Notes: svn path=/head/; revision=38207
* New port: biology/fasta, the FASTA2 suite of DNA and protein sequenceJames E. Housley2001-02-111-0/+1
| | | | | | | | | | search tools PR: 24715 Submitted by: Johann Visagie <johann@egenetics.com> Notes: svn path=/head/; revision=38205
* add gaussian98, an ab-initio molecular orbital calculation program.FUJISHIMA Satsuki2001-02-101-0/+1
| | | | | | | | PR: 23577 Submitted by: NAKATA, Maho <chat95@mbox.kyoto-inet.or.jp> Notes: svn path=/head/; revision=38180
* New Port: biology/ncbi-toolkitJames E. Housley2000-10-291-0/+1
| | | | | | | | | | National Center for Biotechnology Information (NCBI) Development Toolkit. PR: 22388 Submitted by: Tony Maher <tony.maher@ebioinformatics.com> Notes: svn path=/head/; revision=34402
* Initial import of fastDNAml Version 1.2.2James E. Housley2000-10-121-0/+1
| | | | | | | | | | The faster variant of DNAML, makes phylogenetic trees using maximum likelihood PR: 21931 Submitted by: Motomichi Matsuzaki <mzaki@e-mail.ne.jp> Notes: svn path=/head/; revision=33727
* Initial import of biology/biojavaJames E. Housley2000-10-101-0/+1
| | | | | | | | PR: 21678 Submitted by: Brad Chapman <chapmanb@arches.uga.edu> Notes: svn path=/head/; revision=33667
* This is nab (nucleic acid builder), a language for macromoleculesJames E. Housley2000-10-101-0/+1
| | | | | | | | PR: 21585 Submitted by: M. L. Dodson <bdodson@scms.utmb.EDU> Notes: svn path=/head/; revision=33640
* Add emboss, the European Molecular Biology Open Software SuiteNeil Blakey-Milner2000-07-311-0/+1
| | | | | | | | PR: ports/20317 Submitted by: Johann Visagie <johann@egenetics.com> Notes: svn path=/head/; revision=31178
* Add py-biopython, is a collection of Python packages and modules createdNeil Blakey-Milner2000-07-311-0/+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> Notes: svn path=/head/; revision=31163
* Add BioPerl, a collection of Perl5 mods for bioinformatics/genomicsNeil Blakey-Milner2000-07-281-0/+1
| | | | | | | | PR: ports/20252 Submitted by: Johann Visagie <johann@egenetics.com> Notes: svn path=/head/; revision=31084
* Add p5-AcePerl, a perl interface to the ACEDB genome database systemNeil Blakey-Milner2000-07-281-0/+1
| | | | | | | | PR: ports/20223 Submitted by: Johann Visagie <johann@egenetics.com> Notes: svn path=/head/; revision=31083
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