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* SIMAP (Similarity Matrix of Proteins) is a public database of pre-calculatedpav2006-06-191-0/+1
| | | | | | | | | | | | protein similarities that plays a key role in many bioinformatics methods. It contains about all currently published protein sequences and is continuously updated. The computational effort for keeping SIMAP up-to-date is constantly increasing. Please help to update SIMAP by calculating protein similarities on your computer. WWW: http://boinc.bio.wzw.tum.de/boincsimap/
* Adding port biology/p5-Bio-Phylo, Phylogenetic analysis using perl.aaron2006-05-131-0/+1
| | | | Approved by: tobez (implicit)
* Add protomol 2.0.3, OO, component based, framework for molecularehaupt2006-05-051-0/+1
| | | | | | | dynamics (MD) simulations. PR: 95123 Submitted by: Sangwoo Shim <sangwoos@gmail.com>
* Bioperl-run contain modules that provides a PERL interface to variousgarga2006-05-021-0/+1
| | | | | | | | | | bioinformatics applications. This allows various applications to be used with common Bioperl objects. WWW: http://bioperl.org/ PR: ports/93675 Submitted by: Mauricio Herrera Cuadra <mauricio@arareko.net>
* Bioperl-run contain modules that provides a PERL interface to variousgarga2006-05-021-0/+1
| | | | | | | | | | bioinformatics applications. This allows various applications to be used with common Bioperl objects. WWW: http://bioperl.org/ PR: ports/93674 Submitted by: Mauricio Herrera Cuadra <mauricio@arareko.net>
* Add lagan 1.2, efficient tools for large-scale multiple alignments ofgarga2006-03-161-0/+1
| | | | | | | genomic DNA. PR: ports/93058 Submitted by: Fernan Aguero <fernan@iib.unsam.edu.ar>
* Add mafft 5.734, multiple sequence alignments based on fast Fouriergarga2006-03-151-0/+1
| | | | | | | transform. PR: ports/93059 Submitted by: Fernan Aguero <fernan@iib.unsam.edu.ar>
* Add dotter 20021204 # last modified date in FTP server, a viewer forgarga2006-03-151-0/+1
| | | | | | | multiple sequence alignments. PR: ports/93055 Submitted by: Fernan Aguero <fernan@iib.unsam.edu.ar>
* Add blat 33, a fast tool for local sequence similarity searches.garga2006-03-151-0/+1
| | | | | PR: ports/93060 Submitted by: Fernan Aguero <fernan@iib.unsam.edu.ar>
* Add belvu 2.29, a viewer for multiple sequence alignments.garga2006-03-151-0/+1
| | | | | PR: ports/93056 Submitted by: Fernan Aguero <fernan@iib.unsam.edu.ar>
* Jalview is a multiple alignment editor written in Java. It is used widely in ahq2006-02-131-0/+1
| | | | | | | | | | variety of web pages (e.g. the EBI Clustalw server and the Pfam protein domain database) and is also available as a general purpose alignment editor. WWW: http://www.jalview.org PR: 93054 Submitted by: Fernan Aguero <fernan@iib.unsam.edu.ar>
* - Resurrect, update to version 1.5 (literally 1.50 since I wanted to avoiddanfe2006-01-191-0/+1
| | | | | | | | | | | unnecessary PORTEPOCH bump) - Update MASTER_SITES and WWW line, provide backup download site - Come up with better port description - Reset maintainer to ports@ - Uphold CXX and CXXFLAGS - Clean up Makefile slightly - Don't install yet another copy of GPL and texts in French - Add SHA256 hash to distinfo
* - Remove expired portspav2006-01-141-3/+0
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* - Re-add p5-bioperl-devel, development version of biology/p5-bioperlbarner2005-12-021-0/+1
| | | | | | | (A collection of Perl modules for bioinformatics) PR: ports/89497 Submitted by: Mauricio Herrera Cuadra <arareko@yahoo.com>
* Remove expired portskris2005-11-051-1/+0
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* Add p5-Bio-ASN1-EntrezGene, a Regular expression-based Perl Parser forehaupt2005-10-151-0/+1
| | | | | | | | NCBI Entrez Gene. PR: 87423 Submitted by: Mauricio Herrera Cuadra <mauricio@arareko.net> Approved by: novel (mentor) (implicit)
* Add p5-Bio-Das 1.02, client-side library for Distributed Genomegarga2005-09-011-0/+1
| | | | | | | Annotation System. PR: ports/76379 Submitted by: Razi Khaja <razi@genet.sickkids.on.ca>
* - biology/act is redundant after biology/artemis updatesem2005-03-121-1/+0
| | | | | | PR: ports/76217 Submitted by: Fernan Aguero <fernan@iib.unsam.edu.ar> Approved by: maintainer timeout (2 monthes)
* Add finchtv 1.3.0, a chromatogram trace viewer.thierry2005-03-111-0/+1
| | | | | PR: 70271 Submitted by: Fernan Aguero <fernan (at) iib.unsam.edu.ar>
* As previously announced, remove ports that have reached their expiry date,kris2005-02-181-1/+0
| | | | and the handful of ports that depended on them.
* [new port] biology/embassysem2004-11-261-0/+1
| | | | | PR: ports/74330 Submitted by: Fernan Aguero <fernan(at)iib.unsam.edu.ar>
* Add blast, a powerful software package for gene and protein identification,pav2004-11-111-0/+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>
* Add ariadne 1.3, programs to compare protein sequences andkrion2004-06-221-0/+1
| | | | | | | profiles, using the Smith-Waterman algorithm. PR: ports/67811 Submitted by: Fernan Aguero <fernan@iib.unsam.edu.ar>
* Remove category pkg/COMMENT files in favour of a COMMENT variable in thekris2004-04-021-0/+2
| | | | | | | category makefile. Submitted by: Matthew Seaman <m.seaman@infracaninophile.co.uk> PR: 59651
* new port:biology/lsysexpedwin2003-09-031-0/+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>
* As announced on May 6, remove the broken p5-bioperl-devel port.kris2003-08-081-1/+0
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* A new port garlic, free molecular viewer and editor, free molecularmaho2003-07-281-0/+1
| | | | | visualization program, protein structure, DNA structure, PDB, molecular rendering, biological macromolecule.
* Remove gaussian98kris2003-02-051-1/+0
| | | | Pointy hat to: maho
* New Port: biology/actedwin2003-01-161-0/+1
| | | | | PR: ports/35753 Submitted by: Camson Huynh <chuynh@biolateral.com.au>
* add treepuzzle 5.1ijliao2002-11-201-0/+1
| | | | | | | Maximum likelihood phylogeny reconstruction using quartets PR: 45241 Submitted by: Jan Lentfer <lentferj@neslonek.bio.tu-darmstadt.de>
* Connect distribfold to build after moving it from misc categorylioux2002-10-071-0/+1
| | | | | | | Prompted by: kris, Adam Weinberger <adam@vectors.cx>, Fernan Aguero <fernan@iib.unsam.edu.ar>, others
* add primer3 0.9ijliao2002-09-171-0/+1
| | | | | | | Primer3 helps to choose primers for PCR reactions PR: 35298 Submitted by: Tony Maher <tonym@biolateral.com.au>
* Flip is used to find/translate orfs.dinoex2002-09-101-0/+1
| | | | | | WWW: ftp://megasun.bch.umontreal.ca/pub/flip/ PR: 35332 Submitted by: tonym@biolateral.com.au
* "Wise2 is package that is focused on comparing DNA sequences atdinoex2002-09-101-0/+1
| | | | | the level of its conceptual translation, regardless of sequencing error and introns."
* New port L-Breeder version 1.0: Allows you to display and breedlioux2002-08-211-0/+1
| | | | | | | L-system forms PR: 38725 Submitted by: David Yeske <dyeske@yahoo.com>
* Add pymol 0.82, Free and Open-Source molecular modeling system.perky2002-08-131-0/+1
| | | | | PR: 40694 Submitted by: Nakata Maho <chat95@mbox.kyoto-inet.or.jp>
* add libgenome 0.5.0ijliao2002-07-301-0/+1
| | | | Toolkit for developing bioinformatic related software in C++
* 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 interfacedinoex2002-04-021-0/+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
* 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).
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