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* biology/seqtools: Tools for visualising sequence alignmentsWilliam Grzybowski2013-11-101-1/+1
| | | | | | | | | | | | | | | | | | | Blixem is an interactive browser of pairwise alignments that have been stacked up in a "master-slave" multiple alignment; it is not a 'true' multiple alignment but a 'one-to-many' alignment. Belvu is a multiple sequence alignment viewer and phylogenetic tool. Dotter is a graphical dot-matrix program for detailed comparison of two sequences. WWW: http://www.sanger.ac.uk/resources/software/seqtools/ PR: ports/183801 Submitted by: Kurt Jaeger <fbsd-ports opsec.eu> Notes: svn path=/head/; revision=333374
* - Disconnect ports removed in r325546Bryan Drewery2013-08-291-1/+0
| | | | Notes: svn path=/head/; revision=325558
* KDE3 and QT3 expired on 2013-07-01, remove these ports.Rene Ladan2013-07-261-1/+0
| | | | | | | | | | | | | | | | | | | Unfortunately, this also affects some ports using QT3 as a GUI toolkit. Changes to infrastructure files: - bsd.kde.mk : obsolete, remove - bsd.qt.mk : note that a CONFLICTS_BUILD line can probably go after a while - CHANGES : document the removals from bsd.port.mk - KNOBS : remove KDE and QT (KDE4 and QT4 should be used instead) - MOVED : add the removed ports PR: ports/180745 Submitted by: rene Approved by: portmgr (bapt) Exp-run by: bapt Notes: svn path=/head/; revision=323748
* Add Unipro UGENE, a free open-source crowss-platform bioinformatics software.Alexey Dokuchaev2013-02-231-0/+1
| | | | | | | | PR: ports/173387 Submitted by: Hannes Hauswedell Notes: svn path=/head/; revision=312798
* 2012-11-26 benchmarks/gsbench: No more public distfilesBaptiste Daroussin2012-11-281-1/+0
| | | | | | | | | | | | | | 2012-11-26 benchmarks/xengine: No more public distfiles 2012-11-26 biology/belvu: No more public distfiles 2012-11-26 multimedia/kaffeine-mozilla: No more public distfiles 2012-11-26 www/gnustep-ticker: Abandonware 2012-11-26 net/tryst-examples: Abandonware 2012-11-26 net/tryst: Abandonware Feature safe: yes Notes: svn path=/head/; revision=307892
* 2012-10-20 chinese/wangttf: No more public distfilesBaptiste Daroussin2012-10-251-1/+0
| | | | | | | | | | | | | 2012-10-20 chinese/stardict-dict-zh_TW: No more public distfiles 2012-10-20 chinese/stardict-dict-zh_CN: No more public distfiles 2012-10-20 chinese/mingunittf: No more public distfiles 2012-10-20 chinese/dfsongsd: No more public distfiles 2012-10-20 biology/dna-qc: No more public distfiles Feature safe: yes Notes: svn path=/head/; revision=306411
* Add new ports biology/plink [1] and biology/plinkseq [2]:Max Brazhnikov2012-09-271-0/+2
| | | | | | | | | | | | | PLINK is a free, open-source whole genome association analysis toolset. PLINK/SEQ is an open-source C/C++ library for working with human genetic variation data. PR: ports/171918 [1] PR: ports/171922 [2] Submitted by: Jason Bacon <jwbacon at tds.net> Notes: svn path=/head/; revision=304954
* SeqAn is an open source C++ library of efficient algorithmsDmitry Marakasov2012-06-061-0/+1
| | | | | | | | | | | | | | and data structures for the analysis of sequences with the focus on biological data. The library is licensed under the 3-clause BSD license except the applications which are GPL. WWW: http://www.seqan.de/ PR: 167571 Submitted by: Hannes <h2+fbsdports@fsfe.org> Notes: svn path=/head/; revision=298619
* Bye bye abandonwares (part 2)Baptiste Daroussin2011-08-011-5/+0
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | 2011-08-01 benchmarks/rawio: Looks like an abandonware, no more public distfiles 2011-08-01 benchmarks/tmetric: Looks like abandonware, no more public distfiles 2011-08-01 biology/L-Breeder: Looks like an abandonware, no more public distfile 2011-08-01 biology/crimap: Looks like an abandonware, no more public distfile 2011-08-01 biology/distribfold: No more upstream, looks like an abandonware 2011-08-01 biology/kinemage: Looks like an abandonware, no more public distfile 2011-08-01 biology/lsysexp: Looks like an abandonware, no more public distfile 2011-08-01 chinese/chm2html: Looks like an abandonware, no more public distfile 2011-08-01 chinese/ntuttf: No more public distfiles available 2011-08-01 chinese/reciteword: Looks like an abandonware, no more public distfile 2011-08-01 chinese/tocps: No more pulic distfiles 2011-08-01 chinese/xttmgr: Looks like an abandonware, no more public distfile 2011-08-01 comms/mserver: Looks like an abandonware, no more public distfiles 2011-08-01 comms/qicosi: Looks like an abandonware, no more public distfile 2011-08-01 comms/sms_client: Looks like an abandonware, no more public distfile 2011-08-01 comms/smstools: Looks like an abandonware, no more public distfile 2011-08-01 converters/siconv: Looks like an abandonware, no more public distfiles 2011-08-01 converters/utf8conv: Looks like an abandonware, no more public distfile 2011-08-01 databases/pgcluster: Looks like an abandonware, no more public distfile 2011-08-01 databases/py-MySQL: Please use databases/py-MySQLdb instead 2011-08-01 databases/py-SQLDict: Looks like an abandonware, no more public distfile 2011-08-01 databases/py-rrdpipe: Looks like an abandonware, no more public distfile 2011-08-01 databases/sybase_ase: no more public distfiles available Notes: svn path=/head/; revision=278678
* Bio::GFF3 are low-level, fast functions for parsing GFF version 3 files.Wen Heping2011-04-221-0/+1
| | | | | | | | | | All they do is convert back and forth between low-level Perl data structures and GFF3 text. WWW: http://search.cpan.org/dist/Bio-GFF3/ Notes: svn path=/head/; revision=273031
* p5-Bio-Das-Lite is an implementation of a client for the DAS protocol (XMLWen Heping2010-03-011-0/+1
| | | | | | | | | | | over HTTP primarily for biological-data). WWW: http://search.cpan.org/dist/Bio-Das-Lite/ Feature safe: yes Notes: svn path=/head/; revision=250445
* python-nexus is a generic nexus (phylogenetics) file format(.nex, .trees)Wen Heping2009-12-291-0/+1
| | | | | | | | | reader for python. WWW: http://simon.net.nz/articles/python-nexus Notes: svn path=/head/; revision=246859
* pyfasta is a python module for fast, memory-efficient, pythonicWen Heping2009-11-181-0/+1
| | | | | | | | | access to fasta sequence files. WWW: http://bitbucket.org/brentp/biostuff/src/ Notes: svn path=/head/; revision=244412
* Velvet is a de novo genomic assembler specially designed for short readDmitry Marakasov2009-11-071-0/+1
| | | | | | | | | | | | | | | | | | sequencing technologies, such as Solexa or 454, developed by Daniel Zerbino and Ewan Birney at the European Bioinformatics Institute (EMBL-EBI). Citation: Velvet: algorithms for de novo short read assembly using de Bruijn graphs. D.R. Zerbino and E. Birney. Genome Research 18: 821-829 (2008) WWW: http://www.ebi.ac.uk/~zerbino/velvet/ PR: 140147 Submitted by: Motomichi Matsuzaki <mzaki@m.u-tokyo.ac.jp> Notes: svn path=/head/; revision=243919
* Bio::SCF module allows you to read and update (in a restrictedMartin Wilke2009-08-281-0/+1
| | | | | | | | | | | | | | way) SCF chromatographic sequence files. It is an interface to Roger Staden's io-lib. See the installation directions for further instructions. WWW: http://search.cpan.org/dist/Bio-SCF/ PR: ports/138263 Submitted by: Wen Heping <wenheping at gmail.com> Notes: svn path=/head/; revision=240489
* Io_lib is a library of file reading and writing code to provide aMartin Wilke2009-08-281-0/+1
| | | | | | | | | | | | | | | general purpose trace file (and Experiment File) reading interface. The programmer simply calls the (eg) read_reading to create a "Read" C structure with the data loaded into memory. It has been compiled and tested on a variety of unix systems, MacOS X and MS Windows. WWW: http://staden.sourceforge.net/ PR: ports/138254 Submitted by: Wen Heping <wenheping at gmail.com> Notes: svn path=/head/; revision=240487
* Bio::NEXUS package provides an object-oriented, Perl-basedMartin Wilke2009-08-221-0/+1
| | | | | | | | | | | | | | | | | | | | | | applications programming interface (API) to the NEXUS file format of Maddison, et al., 1997 (Syst. Biol. 46:590-621). NEXUS is a powerful and extensible format designed for use in evolutionary analysis, including the analysis of molecular sequence data as well as classical morphological and life-history data. NEXUS is the input or output format for software such as PAUP*, MacClade, Mesquite, SIMMAP, MrBayes, Nexplorer, and so on. This package also contains the demonstration applications nexplot.pl (plot character data with a tree) and nextool.pl (allowing programmatic editing, e.g., selecting particular clades or subsets of data). WWW: http://search.cpan.org/dist/Bio-NEXUS/ PR: ports/137983 Submitted by: Wen Heping <wenheping at gmail.com> Notes: svn path=/head/; revision=240135
* PhyML is a software that estimates maximum likelihood phylogenies fromDmitry Marakasov2009-07-211-0/+1
| | | | | | | | | | | | | | | | | | | | | | | | | | alignments of nucleotide or amino acid sequences. It provides a wide range of options that were designed to facilitate standard phylogenetic analyses. The main strengths of PhyML lies in the large number of substitution models coupled to various options to search the space of phylogenetic tree topologies, going from very fast and efficient methods to slower but generally more accurate approaches. It also implements two methods to evaluate branch supports in a sound statistical framework (the non-parametric bootstrap and the approximate likelihood ratio test). PhyML was designed to process moderate to large data sets. In theory, alignments with up to 4,000 sequences 2,000,000 character-long can analyzed. In practice however, the amount of memory required to process a data set is proportional of the product of the number of sequences by their length. Hence, a large number of sequences can only be processed provided that they are short. Also, PhyML can handle long sequences provided that they are not numerous. With most standard personal computers, the "comfort zone" for PhyML generally lies around 3 to 500 sequences less than 2,000 character long. WWW: http://code.google.com/p/phyml/ PR: 136877 Submitted by: Ben Allen <ben@sysadminschronicles.com> Notes: svn path=/head/; revision=238140
* p5-Bio-MAGETAB contains the core MAGE-TAB Utilities Perl modules. ThisMartin Wilke2009-07-011-0/+1
| | | | | | | | | | | | | | | | is a beta release. All functions have now been implemented and most have test suites; the exceptions include the modules involved in export of MAGE-TAB documents, which are still a little experimental in nature. The API is mostly finalised (and fully documented), but some details may yet change where necessary to improve usability. WWW: http://search.cpan.org/dist/Bio-MAGETAB/ PR: ports/136021 Submitted by: Wen Heping <wenheping at gmail.com> Notes: svn path=/head/; revision=236853
* PyCogent is a software library for genomic biology. It is a fully integratedMartin Wilke2009-06-221-0/+1
| | | | | | | | | | | | | | | | | and thoroughly tested framework for: controlling third-party applications; devising workflows; querying databases; conducting novel probabilistic analyses of biological sequence evolution; and generating publication quality graphics. It is distinguished by many unique built-in capabilities (such as true codon alignment) and the frequent addition of entirely new methods for the analysis of genomic data. WWW: http://pycogent.sourceforge.net/ PR: ports/135863 Submitted by: Wen Heping <wenheping at gmail.com> Notes: svn path=/head/; revision=236469
* Add the biology/crux port.Jason Evans2009-06-081-0/+1
| | | | Notes: svn path=/head/; revision=235460
* 2009-05-31 biology/p5-bioperl-devel: no longer under developmentMartin Wilke2009-06-051-2/+0
| | | | | | | | | 2009-05-31 biology/p5-bioperl-run-devel: no longer under development 2009-06-01 net-p2p/deluge05: use net-p2p/deluge instead 2009-06-03 textproc/gmat: failed to build for a long time, no maintainer and apparently no users either Notes: svn path=/head/; revision=235227
* LibSBML is an open-source programming library to help you read, write,Martin Wilke2009-05-281-0/+1
| | | | | | | | | | | | | | | | | | | manipulate, translate, and validate SBML files and data streams. It is not an application itself (though it does come with example programs), but rather a library you can embed in your own applications. LibSBML understands all Levels and Versions of SBML, as well as the SBML Layout proposal by Gauges, Rost, Sahle and Wegner. It's written in ISO C and C++ but can be used from all the languages listed in the right-hand box. WWW: http://www.sbml.org/ PR: ports/135022 Submitted by: Wen Heping <wenheping at gmail.com> Notes: svn path=/head/; revision=234730
* Bio::Glite is an interface to G-language Genome Analysis EnvironmentMartin Wilke2009-04-021-0/+1
| | | | | | | | | | | | | | | | | | | | | | | | | | through its REST web service (http://www.g-language.org). This module allows almost everything G-language GAE can do, without installing all necessary tookits and modules. Advantage of this module over the standard installation of G-language GAE package is: 1. Easy installation from CPAN 2. Extremely light-weight (less than 1000 lines of code) 3. Does not require much CPU/RAM (all calculation is done on the cloud) Disadvantages includes: 1. Slower analysis speed 2. Internet connection is required 3. No other software interfaces such as the G-language Shell WWW: http://search.cpan.org/dist/Bio-Glite/ PR: ports/133273 Submitted by: Wen Heping <wenheping at gmail.com> Notes: svn path=/head/; revision=231492
* p5-Bio-Graphics is a simple GD-based renderer (diagram drawer)Martin Wilke2009-03-101-0/+1
| | | | | | | | | | | | for DNA and protein sequences. WWW: http://search.cpan.org/dist/Bio-Graphics/ PR: ports/132088 Submitted by: Wen Heping <wenheping at gmail.com> Notes: svn path=/head/; revision=229849
* - Delete biology/nab port after being marked DEPRECATED for three monthsPav Lucistnik2008-07-241-1/+0
| | | | | | | | PR: ports/125891 Submitted by: M. L. Dodson <mldodson@comcast.net> (maintainer) Notes: svn path=/head/; revision=217415
* SSAHA is a software tool for very fast matching and alignment of DNAFelippe de Meirelles Motta2008-06-211-0/+1
| | | | | | | | | | | | | | | | sequences. It stands for Sequence Search and Alignment by Hashing Algorithm. It achieves its fast search speed by converting sequence information into a `hash table' data structure, which can then be searched very rapidly for matches. WWW: http://www.sanger.ac.uk/Software/analysis/SSAHA/ PR: ports/124525 Submitted by: Fernan Aguero <fernan@iib.unsam.edu.ar> Approved by: gabor (mentor, implicit) Notes: svn path=/head/; revision=215429
* New port: biology/consed viewing and editing workbench for sequenceEdwin Groothuis2008-05-241-0/+1
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | assembly Consed is a tool for viewing, editing, and finishing sequence assemblies. The port is constituted of 4 parts: biology/phred: base caller with quality evaluation biology/phrap: sequence assembler for shotgun sequencing biology/consed: workbench biology/phd2fasta: small utility All these can be used separately; however, most function of consed depends on the others. Although these programs are licensed freely for academic and nonprofit purposes, users have to contact the authors to get the softwares. Phred (including phd2fasta) and phrap are emailed, and consed can be downloaded to a restricted IP address. For commercial users, the licensing fee is ca. $10,000 at the time of writing. PR: ports/118548 Submitted by: Motomichi Matsuzaki <mzaki@biol.s.u-tokyo.ac.jp> Notes: svn path=/head/; revision=213596
* New port: biology/consed viewing and editing workbench for sequenceEdwin Groothuis2008-05-241-0/+1
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | assembly Consed is a tool for viewing, editing, and finishing sequence assemblies. The port is constituted of 4 parts: biology/phred: base caller with quality evaluation biology/phrap: sequence assembler for shotgun sequencing biology/consed: workbench biology/phd2fasta: small utility All these can be used separately; however, most function of consed depends on the others. Although these programs are licensed freely for academic and nonprofit purposes, users have to contact the authors to get the softwares. Phred (including phd2fasta) and phrap are emailed, and consed can be downloaded to a restricted IP address. For commercial users, the licensing fee is ca. $10,000 at the time of writing. PR: ports/118548 Submitted by: Motomichi Matsuzaki <mzaki@biol.s.u-tokyo.ac.jp> Notes: svn path=/head/; revision=213594
* New port: biology/consed viewing and editing workbench for sequenceEdwin Groothuis2008-05-241-0/+1
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | assembly Consed is a tool for viewing, editing, and finishing sequence assemblies. The port is constituted of 4 parts: biology/phred: base caller with quality evaluation biology/phrap: sequence assembler for shotgun sequencing biology/consed: workbench biology/phd2fasta: small utility All these can be used separately; however, most function of consed depends on the others. Although these programs are licensed freely for academic and nonprofit purposes, users have to contact the authors to get the softwares. Phred (including phd2fasta) and phrap are emailed, and consed can be downloaded to a restricted IP address. For commercial users, the licensing fee is ca. $10,000 at the time of writing. PR: ports/118548 Submitted by: Motomichi Matsuzaki <mzaki@biol.s.u-tokyo.ac.jp> Notes: svn path=/head/; revision=213592
* New port: biology/consed viewing and editing workbench for sequenceEdwin Groothuis2008-05-241-0/+1
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | assembly Consed is a tool for viewing, editing, and finishing sequence assemblies. The port is constituted of 4 parts: biology/phred: base caller with quality evaluation biology/phrap: sequence assembler for shotgun sequencing biology/consed: workbench biology/phd2fasta: small utility All these can be used separately; however, most function of consed depends on the others. Although these programs are licensed freely for academic and nonprofit purposes, users have to contact the authors to get the softwares. Phred (including phd2fasta) and phrap are emailed, and consed can be downloaded to a restricted IP address. For commercial users, the licensing fee is ca. $10,000 at the time of writing. PR: ports/118548 Submitted by: Motomichi Matsuzaki <mzaki@biol.s.u-tokyo.ac.jp> Notes: svn path=/head/; revision=213590
* NJplot is a tree drawing program able to draw any phylogenetic tree expressedPav Lucistnik2008-05-141-0/+1
| | | | | | | | | | | | | | | | | | | | | | | | | in the Newick phylogenetic tree format (e.g., the format used by the PHYLIP package). NJplot is especially convenient for rooting the unrooted trees obtained from parsimony, distance or maximum likelihood tree-building methods. The package contains the following programs: njplot - draw phylogenetic trees and interactively modify them newicktops - non-interactive version rendering into a PostScript file newicktotxt - non-interactive version rendering into a text file unrooted - draw unrooted circular trees If you use NJplot in a published work, please cite the following reference: Perriere, G. and Gouy, M. (1996) WWW-Query: An on-line retrieval system for biological sequence banks. Biochimie, 78, 364-369. WWW: http://pbil.univ-lyon1.fr/software/njplot.html PR: ports/118438 Submitted by: Motomichi Matsuzaki <mzaki@biol.s.u-tokyo.ac.jp> Notes: svn path=/head/; revision=213034
* MUSCLE is multiple alignment software for protein and nucleotide sequences.Pav Lucistnik2008-05-141-0/+1
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | The name stands for multiple sequence comparison by log-expectation. A range of options is provided that give you the choice of optimizing accuracy, speed, or some compromise between the two. Default parameters are those that give the best average accuracy in the published tests. MUSCLE can achieve both better average accuracy and better speed than CLUSTALW or T-Coffee, depending on the chosen options. Citation: Edgar, R. C. (2004) MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Research 32(5): 1792-1797. Edgar, R. C. (2004) MUSCLE: a multiple sequence alignment method with reduced time and space complexity. BMC Bioinformatics 5(1): 113. The NAR paper gives only a brief overview of the algorithm and implementation details. For a full discussion of the method and many of the non-default options that it offers, please see the BMC paper. WWW: http://www.drive5.com/muscle/ PR: ports/118460 Submitted by: Motomichi Matsuzaki <mzaki@biol.s.u-tokyo.ac.jp> Notes: svn path=/head/; revision=213031
* MAPMAKER/EXP is a linkage analysis package designed to help construct primaryRong-En Fan2008-04-061-0/+1
| | | | | | | | | | | | | | | | | | | | | linkage maps of markers segregating in experimental crosses. MAPMAKER/EXP performs full multipoint linkage analysis (simultaneous estimation of all recombination fractions from the primary data) for dominant, recessive, and co- dominant (e.g. RFLP-like) markers. MAPMAKER/EXP is an experimental-cross-only successor to the original MAPMAKER program. MAPMAKER/QTL is a companion program to MAPMAKER/EXP which allows one to map genes controlling polygenic quantitative traits in F2 intercrosses and BC1 backcrosses relative to a genetic linkage map. More information on MAPMAKER/QTL can be found in the technical report (included with MAPMAKER/QTL). WWW: http://www.broad.mit.edu/ftp/distribution/software/mapmaker3/ PR: ports/122452 Submitted by: Tassilo Philipp <tphilipp at potion-studios.com> Notes: svn path=/head/; revision=210625
* MrBayes is a program for the Bayesian estimation of phylogeny.Martin Wilke2007-12-151-0/+1
| | | | | | | | | | | | | | | | | | Bayesian inference of phylogeny is based upon a quantity called the posterior probability distribution of trees, which is the probability of a tree conditioned on the observations. The conditioning is accomplished using Bayes's theorem. The posterior probability distribution of trees is impossible to calculate analytically; instead, MrBayes uses a simulation technique called Markov chain Monte Carlo (or MCMC) to approximate the posterior probabilities of trees. WWW: http://mrbayes.csit.fsu.edu/ PR: ports/118542 Submitted by: mzaki at biol.s.u-tokyo.ac.jp Notes: svn path=/head/; revision=203737
* MUMmer is a modular system for the rapid whole genome alignment of finishedMartin Wilke2007-12-141-0/+1
| | | | | | | | | | | | | | or draft sequence. This package provides an efficient suffix tree library, seed-and-extend alignment, SNP detection, repeat detection, and visualization tools. WWW: http://mummer.sourceforge.net/ PR: ports/118142 Submitted by: Tony Maher Notes: svn path=/head/; revision=203638
* - Sort category MakefilesAndrew Pantyukhin2007-10-051-2/+2
| | | | | | | | Inspired by: Jason Harris <jharris@widomaker.com> Howto: http://twiki.cenkes.org/Cenkes/SortingCategoryMakefiles Notes: svn path=/head/; revision=200970
* Remove expired leaf port:Vasil Dimov2007-01-251-1/+0
| | | | | | | | | | | | 2007-01-07 biology/coalesce: distfile disappeared from homepage Actually the software is still available at: http://evolution.gs.washington.edu/lamarc/coalesce.html, but it is not supported by the authors. Last version is from 1995 and biology/fluctuate can be used instead. Notes: svn path=/head/; revision=183249
* The BioCocoa framework provides developers with the opportunity to addDirk Meyer2006-12-301-0/+1
| | | | | | | | | | | | support for reading and writing BEAST, Clustal, EMBL, Fasta, GCG-MSF, GDE, Hennig86, NCBI, NEXUS, NONA, PDB, Phylip, PIR, Plain/Raw, Swiss-Prot and TNT files by writing only three lines of code. The framework is written in Cocoa (Objective-C). WWW: http://bioinformatics.org/biococoa/ Notes: svn path=/head/; revision=181036
* Adun is a new extendible molecular simulation program that alsoDirk Meyer2006-11-091-0/+1
| | | | | | | | | | | includes data management and analysis capabilities. WWW: http://diana.imim.es/Adun Submitted by: Gürkan Sengün Reviewed by: dinoex Notes: svn path=/head/; revision=176957
* Add gmap 2006.04.21, a Genomic Mapping and Alignment Program for mRNACheng-Lung Sung2006-09-291-0/+1
| | | | | | | | | | and EST Sequences. PR: ports/103651 Submitted by: Bob Zimmermann <rpz at cse.wustl.edu> Notes: svn path=/head/; revision=174086
* Folding@Home is a distributed computing project -- people from through out thePav Lucistnik2006-08-281-0/+1
| | | | | | | | | | | | | | | | | world download and run software to band together to make one of the largest supercomputers in the world. Every computer makes the project closer to our goals. Folding@Home uses novel computational methods coupled to distributed computing, to simulate problems thousands to millions of times more challenging than previously achieved. WWW: http://folding.standford.edu PR: ports/101235 Submitted by: Yonatan <onatan@gmail.com> Notes: svn path=/head/; revision=171590
* SIMAP (Similarity Matrix of Proteins) is a public database of pre-calculatedPav Lucistnik2006-06-191-0/+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/ Notes: svn path=/head/; revision=165801
* Adding port biology/p5-Bio-Phylo, Phylogenetic analysis using perl.Aaron Dalton2006-05-131-0/+1
| | | | | | | Approved by: tobez (implicit) Notes: svn path=/head/; revision=162248
* Add protomol 2.0.3, OO, component based, framework for molecularEmanuel Haupt2006-05-051-0/+1
| | | | | | | | | | dynamics (MD) simulations. PR: 95123 Submitted by: Sangwoo Shim <sangwoos@gmail.com> Notes: svn path=/head/; revision=161442
* Bioperl-run contain modules that provides a PERL interface to variousRenato Botelho2006-05-021-0/+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> Notes: svn path=/head/; revision=161215
* Bioperl-run contain modules that provides a PERL interface to variousRenato Botelho2006-05-021-0/+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> Notes: svn path=/head/; revision=161213
* Add lagan 1.2, efficient tools for large-scale multiple alignments ofRenato Botelho2006-03-161-0/+1
| | | | | | | | | | genomic DNA. PR: ports/93058 Submitted by: Fernan Aguero <fernan@iib.unsam.edu.ar> Notes: svn path=/head/; revision=157464
* Add mafft 5.734, multiple sequence alignments based on fast FourierRenato Botelho2006-03-151-0/+1
| | | | | | | | | | transform. PR: ports/93059 Submitted by: Fernan Aguero <fernan@iib.unsam.edu.ar> Notes: svn path=/head/; revision=157209
* Add dotter 20021204 # last modified date in FTP server, a viewer forRenato Botelho2006-03-151-0/+1
| | | | | | | | | | multiple sequence alignments. PR: ports/93055 Submitted by: Fernan Aguero <fernan@iib.unsam.edu.ar> Notes: svn path=/head/; revision=157195
generated by cgit v1.2.3 (git 2.25.1) at 2025-01-13 17:16:11 +0000