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>
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
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>
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>
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>
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>
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>
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>
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>
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
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>
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>
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)
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>
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>
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>
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>
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>
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>
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>
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
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
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.
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/
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>
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/
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>
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>
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>
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
