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
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>
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>
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
