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>
-Update libtool and libltdl to 2.2.6a.
-Remove devel/libtool15 and devel/libltdl15.
-Fix ports build with libtool22/libltdl22.
-Bump ports that depend on libltdl22 due to shared library version change.
-Explain what to do update in the UPDATING.
It has been tested with GNOME2, XFCE4, KDE3, KDE4 and other many wm/desktop
and applications in the runtime.
With help: marcus and kwm
Pointyhat-exp: a few times by pav
Tested by: pgollucci, "Romain Tartière" <romain@blogreen.org>, and
a few MarcusCom CVS users. Also, I might have missed a few.
Repocopy by: marcus
Approved by: portmgr
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>
modular xorg.
- supply corresponding USE_XORG for all imake-using ports that need it
- USE_IMAKE no longer implies USE_XLIB in absence of USE_XORG
- retire USE_X_PREFIX which is not really used anywhere after the
above change
- a few minor nits like whitespace and SF macro
Tested by: 2 tinderbox runs by pav
Approved by: portmgr (pav)
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>
both current (fc4) and future linux (f8) distributions at one
ports tree.
The patch contains full changes to ports/Mk files and all ports involved.
But only infrastructure is changed. The resulting packages are the same as
before. Hence no need to bump PORTREVISIONs.
The idea was taken from bsd.gnome.mk and others.
More than 130 ports are switched to follow a new linux infrastructure
introduced by changes to bsd.port.mk, bsd.linux-rpm.mk and a new
bsd.linux-apps.mk.
Thanks for all who was involved and helped me with this work.
And help from Alexander Leidinger was incredible.
Other changes are coming. Stay tuned!
PR: ports/132510
Submitted by: bsam (me)
Exp-run by: portmgr (pav)
- Bump PORTREVISION for all ports depending on libglut since the shlib
version number went from 4 to 3.
- Bump PORTREVISION for all ports depending on libXaw as libXaw.so.8 isn't
installed anymore.
- Couple of ports fixes (mostly missing xorg components added to USE_XORG).
re-rolled.
- Move post-patch target into files/patch-xwin.c to remove sed invocation.
- Respect NOPORTDATA and DATADIR.
- Bring files/patch-aa back (to preserve history) and retire patch-makefile.
- Fixup files/patch-xwin.c so it applies cleanly to this version.
Specifically, newer autoconf (> 2.13) has different semantic of the
configure target. In short, one should use --build=CONFIGURE_TARGET
instead of CONFIGURE_TARGET directly. Otherwise, you will get a warning
and the old semantic may be removed in later autoconf releases.
To workaround this issue, many ports hack the CONFIGURE_TARGET variable
so that it contains the ``--build='' prefix.
To solve this issue, under the fact that some ports still have
configure script generated by the old autoconf, we use runtime detection
in the do-configure target so that the proper argument can be used.
Changes to Mk/*:
- Add runtime detection magic in bsd.port.mk
- Remove CONFIGURE_TARGET hack in various bsd.*.mk
- USE_GNOME=gnometarget is now an no-op
Changes to individual ports, other than removing the CONFIGURE_TARGET hack:
= pkg-plist changed (due to the ugly CONFIGURE_TARGET prefix in * executables)
- comms/gnuradio
- science/abinit
- science/elmer-fem
- science/elmer-matc
- science/elmer-meshgen2d
- science/elmerfront
- science/elmerpost
= use x86_64 as ARCH
- devel/g-wrap
= other changes
- print/magicfilter
GNU_CONFIGURE -> HAS_CONFIGURE since it's not generated by autoconf
Total # of ports modified: 1,027
Total # of ports affected: ~7,000 (set GNU_CONFIGURE to yes)
PR: 126524 (obsoletes 52917)
Submitted by: rafan
Tested on: two pointyhat 7-amd64 exp runs (by pav)
Approved by: portmgr (pav)
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)
The affected ports are the ones with gettext as a run-dependency
according to ports/INDEX-7 (5007 of them) and the ones with USE_GETTEXT
in Makefile (29 of them).
PR: ports/124340
Submitted by: edwin@
Approved by: portmgr (pav)
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>
- Remove USE_XLIB/USE_X_PREFIX/USE_XPM in favor of USE_XORG
- Remove X11BASE support in favor of LOCALBASE or PREFIX
- Use USE_LDCONFIG instead of INSTALLS_SHLIB
- Remove unneeded USE_GCC 3.4+
Thanks to all Helpers:
Dmitry Marakasov, Chess Griffin, beech@, dinoex, rafan, gahr,
ehaupt, nox, itetcu, flz, pav
PR: 116263
Tested on: pointyhat
Approved by: portmgr (pav)
