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61 Commits

Author SHA1 Message Date
Kris Kennaway
736746419e As announced on May 6, remove the broken p5-bioperl-devel port. 2003-08-08 03:31:11 +00:00
Maho Nakata
4dd4b89f44 A new port garlic, free molecular viewer and editor, free molecular 
visualization program, protein structure, DNA structure, PDB,
molecular rendering, biological macromolecule.
 2003-07-28 06:38:37 +00:00
Kris Kennaway
1140e88185 Remove gaussian98 
Pointy hat to:	maho
 2003-02-05 09:01:06 +00:00
Edwin Groothuis
b7eafb33b6 New Port: biology/act 
PR:		ports/35753
Submitted by:	Camson Huynh <chuynh@biolateral.com.au>
 2003-01-16 14:22:59 +00:00
Ying-Chieh Liao
545bf7ae46 add treepuzzle 5.1 
Maximum likelihood phylogeny reconstruction using quartets

PR:		45241
Submitted by:	Jan Lentfer <lentferj@neslonek.bio.tu-darmstadt.de>
 2002-11-20 08:54:10 +00:00
Mario Sergio Fujikawa Ferreira
72353480ab Connect distribfold to build after moving it from misc category 
Prompted by:	kris,
		Adam Weinberger <adam@vectors.cx>,
		Fernan Aguero <fernan@iib.unsam.edu.ar>,
		others
 2002-10-07 03:07:59 +00:00
Ying-Chieh Liao
47be6d4a10 add primer3 0.9 
Primer3 helps to choose primers for PCR reactions

PR:		35298
Submitted by:	Tony Maher <tonym@biolateral.com.au>
 2002-09-17 15:31:09 +00:00
Dirk Meyer
f593f06ed2 Flip is used to find/translate orfs. 
WWW: ftp://megasun.bch.umontreal.ca/pub/flip/
PR:		35332
Submitted by:	tonym@biolateral.com.au
 2002-09-10 14:04:06 +00:00
Dirk Meyer
ce85742f4f "Wise2 is package that is focused on comparing DNA sequences at 
the level of its conceptual translation, regardless of sequencing
error and introns."
 2002-09-10 13:58:40 +00:00
Mario Sergio Fujikawa Ferreira
e3aab5688e New port L-Breeder version 1.0: Allows you to display and breed 
L-system forms

PR:		38725
Submitted by:	David Yeske <dyeske@yahoo.com>
 2002-08-21 00:01:59 +00:00
Hye-Shik Chang
dc8e3f8160 Add pymol 0.82, Free and Open-Source molecular modeling system. 
PR:		40694
Submitted by:	Nakata Maho <chat95@mbox.kyoto-inet.or.jp>
 2002-08-13 11:53:43 +00:00
Ying-Chieh Liao
e2e513a934 add libgenome 0.5.0 
Toolkit for developing bioinformatic related software in C++
 2002-07-30 10:57:06 +00:00
Ying-Chieh Liao
9e3da593d2 add avida 1.6.0 
Avida is an auto-adaptive genetic system designed for ALife research

PR:		37268
Submitted by:	Jeremy Karlson <karlj000@unbc.ca>
 2002-04-20 15:17:46 +00:00
Dirk Meyer
3e70b923da Swiss-PdbViewer is an application that provides a user friendly interface 
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
 2002-04-02 16:18:53 +00:00
Johann Visagie
c6d9b64615 Add crimap 2.4, a tool for the creation of multilocus linkage maps. 
PR:		35198
Submitted by:	Tony Maher <tonym@biolateral.com.au>
 2002-03-27 14:42:56 +00:00
Johann Visagie
9e8dd630bc Add tRNAscan-SE 1.21, an improved tool for transfer RNA detection. 
PR:		33853
Submitted by:	chuynh@biolateral.com.au
 2002-03-27 14:18:49 +00:00
Johann Visagie
a3a6a2eb07 Add t_coffee 1.37, a multiple DNA or protein sequence alignment package. 2002-01-25 14:58:16 +00:00
Kevin Lo
30d7b16772 Initial import of artemis 4.0 
Artemis is a  DNA sequence viewer and annotation tool.

PR: 32914
Submitted by: Camson <chuynh@biolateral.com.au>
 2001-12-22 14:39:40 +00:00
Pete Fritchman
74375be19f Add gff2ps 0.97b, converts gff-formated genomic data-sets to 
PostScript.

PR:		32920
Submitted by:	Camson Huynh <chuynh@biolateral.com.au>
 2001-12-19 10:03:26 +00:00
Pete Fritchman
e42a8c9a6e Add dna-qc 1993.07.26, a quality control algorithm for DNA 
sequencing projects.

PR:		32998
Submitted by:	Tony Maher <tonym@biolateral.com.au>
 2001-12-19 03:20:48 +00:00
Akinori MUSHA
b98ad00ebf Add ruby-bio (BioRuby), an integrated environment for Bioinformatics 
written in Ruby.
 2001-10-24 06:21:52 +00:00
Johann Visagie
cdda6a705b Add nclever 4.0, a character-based version of NCBI's Entrez program. 
PR:		30783
Submitted by:	Tony Maher <tonym@biolateral.com.au>
 2001-09-26 09:22:02 +00:00
Johann Visagie
8aff3a669c Add seqio 1.2.2, a set of C functions which can read/write 
biological sequence files.

PR:		29922
Submitted by:	Tony Maher <tonym@biolateral.com.au>
 2001-08-22 12:07:26 +00:00
Johann Visagie
490da9f942 Add treeviewx 0.1.1, a phylogenetic tree viewer. 
PR:		29770
Submitted by:	Tony Maher <tonym@biolateral.com.au>
 2001-08-17 08:39:28 +00:00
Johann Visagie
133a08c54d Add p5-bioperl-devel 0.9.0, 
a collection of Perl modules for
bioinformatics (developer's release).
 2001-08-14 09:36:36 +00:00
Johann Visagie
f7b5a60b9b Add lamarc 2001.08.06, 
a package of programs for computing
population parameters.
 2001-08-07 08:17:58 +00:00
Johann Visagie
043c249d98 Add recombine 1.40, a program to fit population models across sites. 2001-08-06 14:49:53 +00:00
Johann Visagie
52619bca7a Add fluctuate 1.30, a program to fit population models. 2001-08-06 14:45:39 +00:00
Johann Visagie
cd0583a2a8 Add coalesce 1.50, a program to fit population models. 2001-08-06 14:41:58 +00:00
Johann Visagie
199894f656 Add migrate 1.2, 
a program to estimate population sizes and
migration rates.
 2001-08-06 13:07:46 +00:00
Johann Visagie
f046432f9c Add grappa 1.0.2, Genome Rearrangements Analysis and Phylogeny 
Software.

PR:		28541
Submitted by:	dbader@eece.unm.edu
 2001-07-04 08:39:40 +00:00
Ying-Chieh Liao
384048cae5 reimport biology/genpak 2001-02-28 02:46:51 +00:00
Ying-Chieh Liao
d87d30e484 module name conflict with print/gp, so remove it and I'll reimport it again 2001-02-28 02:43:22 +00:00
Ying-Chieh Liao
ca27237a16 add gp 
GP is a set of small utilities to manipulate DNA sequences
 2001-02-27 17:22:29 +00:00
James E. Housley
a3686c5ead - New port: biology/fasta3, which comprises the FASTA3 suite of DNA and 
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>
 2001-02-11 16:28:59 +00:00
James E. Housley
c82fc94311 New port: biology/fasta, the FASTA2 suite of DNA and protein sequence 
search tools

PR:		24715
Submitted by:	Johann Visagie <johann@egenetics.com>
 2001-02-11 16:24:18 +00:00
FUJISHIMA Satsuki
d705c4a51d add gaussian98, an ab-initio molecular orbital calculation program. 
PR:             23577
Submitted by:   NAKATA, Maho <chat95@mbox.kyoto-inet.or.jp>
 2001-02-10 19:38:20 +00:00
James E. Housley
72c15a6ba2 New Port: biology/ncbi-toolkit 
National Center for Biotechnology Information (NCBI) Development Toolkit.

PR:		22388
Submitted by:	Tony Maher <tony.maher@ebioinformatics.com>
 2000-10-29 13:56:24 +00:00
James E. Housley
1bc69d7e0c Initial import of fastDNAml Version 1.2.2 
The faster variant of DNAML, makes phylogenetic trees using maximum likelihood

PR:		21931
Submitted by:	Motomichi Matsuzaki <mzaki@e-mail.ne.jp>
 2000-10-12 12:31:13 +00:00
James E. Housley
1703717285 Initial import of biology/biojava 
PR:		21678
Submitted by:	Brad Chapman <chapmanb@arches.uga.edu>
 2000-10-10 11:14:03 +00:00
James E. Housley
5f2cf6a3fd This is nab (nucleic acid builder), a language for macromolecules 
PR:		21585
Submitted by:	M. L. Dodson <bdodson@scms.utmb.EDU>
 2000-10-10 02:56:57 +00:00
Neil Blakey-Milner
ed9505e0ad Add emboss, the European Molecular Biology Open Software Suite 
PR:		ports/20317
Submitted by:	Johann Visagie <johann@egenetics.com>
 2000-07-31 19:13:54 +00:00
Neil Blakey-Milner
7c7638c998 Add py-biopython, is a collection of Python packages and modules created 
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>
 2000-07-31 12:12:24 +00:00
Neil Blakey-Milner
4634742f54 Add BioPerl, a collection of Perl5 mods for bioinformatics/genomics 
PR:		ports/20252
Submitted by:	Johann Visagie <johann@egenetics.com>
 2000-07-28 14:06:03 +00:00
Neil Blakey-Milner
167641b4f4 Add p5-AcePerl, a perl interface to the ACEDB genome database system 
PR:		ports/20223
Submitted by:	Johann Visagie <johann@egenetics.com>
 2000-07-28 13:16:10 +00:00
Neil Blakey-Milner
7fb6a7b182 Add sim4, an implementation of the sim4 algorithm for aligning expressed 
DNA with genomic sequences

PR:		ports/20219
Submitted by:	Johann Visagie <johann@egenetics.com>
 2000-07-27 14:33:00 +00:00
Alexander Langer
7d609004d5 Add xdrawchem 0.82 - a program for drawing molecules 2000-07-19 13:23:02 +00:00
Steve Price
fdc60854fd Activating the chemeq, clustalw, paml, and phylip ports. 2000-07-10 03:26:57 +00:00
Satoshi Taoka
a6ade68cd4 Added gperiodic and xmolwt 1999-09-06 20:09:12 +00:00
David E. O'Brien
fe1e09a6cc Change Id->FreeBSD. 1999-08-25 04:58:03 +00:00