Bio::FeatureIO is an iterator subsystem for genomic sequence features.
Bio::FeatureIO is a handler module for the formats in the FeatureIO set (eg,
Bio::FeatureIO::GFF). It is the officially sanctioned way of getting at the
format objects, which most people should use.
The Bio::FeatureIO system can be thought of like biological file handles. They
are attached to filehandles with smart formatting rules (eg, GFF format, or BED
format) and can either read or write feature objects (Bio::SeqFeature objects,
or more correctly, Bio::FeatureHolderI implementing objects, of which
Bio::SeqFeature is one such object). If you want to know what to do with a
Bio::SeqFeatureI object, read Bio::SeqFeatureI.
The idea is that you request a stream object for a particular format. All the
stream objects have a notion of an internal file that is read from or written
to. A particular FeatureIO object instance is configured for either input or
output. A specific example of a stream object is the Bio::FeatureIO::gff object.
WWW: http://search.cpan.org/dist/Bio-FeatureIO/
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implementation of genome scale analyses. The library contains a variety of
useful modules, but the particular strengths are:
Classes for reading and working with genome-scale multiple local alignments
(in MAF, AXT, and LAV formats). Generic data structure for indexing on disk
files that contain blocks of data associated with intervals on various
sequences (used, for example, to provide random access to individual
alignments in huge files; optomized for use over network filesystems).
Data structures for working with intervals on sequences:
* "Binned bitsets" which act just like chromosome sized bit arrays,
but lazily allocate regions and allow large blocks of all set or
all unset bits to be stored compactly
* "Intersecter" for performing fast intersection tests that preserve
both query and target intervals and associated annotation
WWW: https://github.com/bxlab/bx-python
PR: 218757
Submitted by: Yuri Victorovich <yuri@rawbw.com>
read and write SAM/BAM/VCF/BCF/BED/GFF/GTF/FASTA/FASTQ files as well as access
to the command line functionality of the samtools and bcftools packages. The
module supports compression and random access through indexing.
This module provides a low-level wrapper around the htslib C-API as using
cython and a high-level API for convenient access to the data within standard
genomic file formats.
WWW: https://pypi.python.org/pypi/pysam
PR: 218745
Submitted by: Yuri Victorovich <yuri@rawbw.com>
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Bio::Coordinate classes are used for working with various biological coordinate
systems. See Bio::Coordinate::Collection and Bio::Collection::Pair for examples.
WWW: http://search.cpan.org/dist/Bio-Coordinate/
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2016-07-04 games/xwordpy: Broken for more than 6 months
2016-07-04 games/netris: Broken for more than 6 months
2016-07-04 games/rt2-demo: Broken for more than 6 months
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2016-07-04 games/live-f1: Broken for more than 6 months
2016-07-04 games/xonix: Broken for more than 6 months
2016-07-04 games/fgkicker: Broken for more than 6 months
2016-07-04 games/tank: Depends on expiring graphics/libaux
2016-07-04 games/linux-nwserver: Broken for more than 6 months
2016-07-04 games/quake2-zaero: Broken for more than 6 months
2016-07-04 games/pyching: Broken for more than 6 months
2016-07-04 games/thevalley: Broken for more than 6 months
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2016-07-04 games/hlstatsx: Broken for more than 6 months
2016-07-04 audio/streamtuner: Broken for more than 6 months
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2016-07-04 audio/alac: Broken for more than 6 months
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2016-07-04 x11-wm/e-module-tclock: Broken for more than 6 months
2016-07-04 x11-wm/musca: Broken for more than 6 months
2016-07-04 x11-wm/e-module-places: Broken for more than 6 months
2016-07-04 x11-wm/e-module-forecasts: Broken for more than 6 months
2016-07-04 x11-wm/e-module-net: Broken for more than 6 months
2016-07-04 x11-wm/e-module-penguins: Broken for more than 6 months
2016-07-04 ftp/fget: Broken for more than 6 months
2016-07-04 net-mgmt/netmond: Broken for more than 6 months
2016-07-04 net-mgmt/ipfm: Broken for more than 6 months
biology/seqan1: create port from current SeqAn 1.3.1 for legacy usage
UPDATING: document SeqAn updates and seqan1 port for legacy usage
PR: 204127
Submitted by: Hannes Hauswedell <h2+fbsdports@fsfe.org>
SeqAn is an open source C++ library of efficient algorithms
and data structures for the analysis of sequences with the
focus on biological data.
This port contains applications built on SeqAn and developed
within the SeqAn project. Among them are famous read mappers
like RazerS and Yara, as well as many other tools. Some
applications are packaged seperately and the library
can be found at biology/seqan.
WWW: http://www.seqan.de/
PR: 204127
Submitted by: Hannes Hauswedell <h2+fbsdports@fsfe.org>
general-use format for representing biological sample by observation contingency
tables. BIOM is a recognized standard for the Earth Microbiome Project and is a
Genomics Standards Consortium supported project.
The BIOM format is designed for general use in broad areas of comparative
-omics. For example, in marker-gene surveys, the primary use of this format is
to represent OTU tables: the observations in this case are OTUs and the matrix
contains counts corresponding to the number of times each OTU is observed in
each sample. With respect to metagenome data, this format would be used to
represent metagenome tables: the observations in this case might correspond to
SEED subsystems, and the matrix would contain counts corresponding to the number
of times each subsystem is observed in each metagenome. Similarly, with respect
to genome data, this format may be used to represent a set of genomes: the
observations in this case again might correspond to SEED subsystems, and the
counts would correspond to the number of times each subsystem is observed in
each genome.
WWW: http://biom-format.org/
PR: 209193
Submitted by: Joseph Mingrone
alignment mode). The speedup over BLAST is up to 20,000 on short reads at a
typical sensitivity of 90-99% relative to BLAST depending on the data and
settings.
WWW: http://ab.inf.uni-tuebingen.de/software/diamond/
PR: 208998
Submitted by: jrm@ftfl.ca
A k-mer is a substring of length k, and counting the occurrences of all such
substrings is a central step in many analyses of DNA sequence. JELLYFISH can
count k-mers quickly by using an efficient encoding of a hash table and by
exploiting the "compare-and-swap" CPU instruction to increase parallelism.
WWW: http://www.genome.umd.edu/jellyfish.html
PR: 207929
Submitted by: bacon4000@gmail.com
Bowtie is an ultrafast, memory-efficient short read aligner. It aligns short
DNA sequences (reads) to the human genome at a rate of over 25 million 35-bp
reads per hour.
This is Bowtie version 2, which will need to coexists with Bowtie 1 for the
foreseeable future. Both are required by certain genomics pipelines, in some
cases (e.g. Trinity) by the same pipeline.
WWW: https://github.com/BenLangmead/bowtie2
PR: 207908
Submitted by: Jason Bacon <bacon4000@gmail.com>
Slclust is a utility that performs single-linkage clustering with the option of
applying a Jaccard similarity coefficient to break weakly bound clusters into
distinct clusters.
WWW: http://sourceforge.net/projects/slclust/
PR: 207997
Submitted by: Jason Bacon <bacon4000@gmail.com>
TransDecoder identifies candidate coding regions within transcript
sequences, such as those generated by de novo RNA-Seq transcript
assembly using Trinity, or constructed based on RNA-Seq alignments
to the genome using Tophat and Cufflinks.
WWW: http://transdecoder.github.io/
PR: 207993
Submitted by: Jason Bacon <bacon4000@gmail.com>
Bowtie is an ultrafast, memory-efficient short read aligner. It aligns short
DNA sequences (reads) to the human genome at a rate of over 25 million 35-bp
reads per hour.
WWW: http://bowtie-bio.sourceforge.net/index.shtml
PR: 206939
Submitted by: Jason Bacon <bacon4000@gmail.com>
A set of tools written in Perl and C++ for working with VCF files, such as
those generated by the 1000 Genomes Project.
WWW: https://github.com/vcftools/vcftools
PR: 206926
Submitted by: Jason Bacon <bacon4000@gmail.com>
genomics analysis tasks. The most widely-used of these tools enable genome
arithmetic, i.e., set theory on the genome. For example, with bedtools one
can intersect, merge, count, complement, and shuffle genomic intervals from
multiple files in common genomic formats such as BAM, BED, GFF/GTF, and VCF.
Although each individual utility is designed to do a relatively simple task,
e.g., intersect two interval files, more sophisticated analyses can be
conducted by stringing together multiple bedtools operations on the command
line or in shell scripts.
WWW: http://bedtools.readthedocs.org/
PR: 204536
Submitted by: scottcheloha@gmail.com
2015-11-26 audio/pecl-id3: Broken for more than 6 months
2015-11-26 dns/geta: Broken for more than 6 months
2015-11-26 finance/openerp-web: Broken for more than 6 months
2015-11-26 devel/py-async: Further using of this module is not encouraged by upstream
2015-11-26 chinese/kon2: Depends on expiring chinese/cce
2015-11-26 games/linux-skulltag: Depends on expiring audio/linux-fmodapi
2015-11-26 archivers/wzip: Broken for more than 6 months
2015-11-26 databases/sybtcl: Broken for more than 6 months
2015-11-26 biology/povchem: Broken for more than 6 months
2015-11-26 audio/btc: Broken for more than 6 months
2015-11-26 astro/wmglobe: Broken for more than 6 months
2015-11-26 graphics/pyro: Broken for more than 6 months
2015-11-26 graphics/jpeg2ps: Broken for more than 6 months
2015-11-26 chinese/gugod-clean: Broken for more than 6 months
2015-11-26 comms/bforce: Broken for more than 6 months
2015-11-26 cad/geda-docs: Broken for more than 6 months
2015-11-26 chinese/cwtexttf: Broken for more than 6 months
2015-11-26 comms/zmtx-zmrx: Broken for more than 6 months
2015-11-26 astro/sky2000: Broken for more than 6 months
2015-11-26 deskutils/libopensync-plugin-file: Broken for more than 6 months
2015-11-26 databases/sqlite-ext-mobigroup: Broken for more than 6 months
2015-11-26 chinese/bg5ps: Broken for more than 6 months
2015-11-26 deskutils/x-tile: Broken for more than 6 months
2015-11-26 graphics/pure-gl: Broken for more than 6 months
2015-11-26 audio/dvda-author: Broken for more than 6 months
2015-11-26 chinese/oxim: Broken for more than 6 months
2015-11-26 editors/spe: Broken for more than 6 months
2015-11-26 audio/mpdscribble: Broken for more than 6 months
2015-11-26 cad/geda-symcheck: Broken for more than 6 months
2015-11-26 audio/linux-fmodapi: Broken for more than 6 months
2015-11-26 audio/pure-audio: Broken for more than 6 months
2015-11-26 editors/bpatch: Broken for more than 6 months
2015-11-26 benchmarks/geekbench: Broken for more than 6 months
2015-11-26 graphics/icoconvert: Broken for more than 6 months
2015-11-26 cad/geda-utils: Broken for more than 6 months
2015-11-26 deskutils/tomboy-plugin-wordcount: Broken for more than 6 months
2015-11-26 graphics/sketch: Broken for more than 6 months
2015-11-26 ftp/spegla: Broken for more than 6 months
2015-11-26 graphics/clutter-box2d: Broken for more than 6 months
2015-11-26 audio/scmpc: Broken for more than 6 months
2015-11-26 ftp/gnusget: Broken for more than 6 months
2015-11-26 comms/gpsk31: Broken for more than 6 months
2015-11-26 cad/geda-gschem: Broken for more than 6 months
2015-11-26 audio/ampache: Broken for more than 6 months
2015-11-26 cad/slffea: Broken for more than 6 months
2015-11-26 audio/cripple: Broken for more than 6 months
2015-11-26 cad/geda-gattrib: Broken for more than 6 months
2015-11-26 cad/findhier: Broken for more than 6 months
2015-11-26 biology/njplot: Broken for more than 6 months
2015-11-26 audio/wmmp: Broken for more than 6 months
2015-11-26 x11/avant-window-navigator: Broken for more than 6 months
2015-11-26 cad/geda-netlist: Broken for more than 6 months
2015-11-26 deskutils/libopensync-plugin-sunbird: Broken for more than 6 months
2015-11-26 biology/ortep3: Broken for more than 6 months
2015-11-26 astro/aa: Broken for more than 6 months
2015-11-26 french/belote: Broken for more than 6 months
2015-11-26 converters/p5-String-SetUTF8: Broken for more than 6 months
2015-11-26 cad/geda-examples: Broken for more than 6 months
2015-11-26 editors/yasnippet: Broken for more than 6 months
2015-11-26 audio/musica: Broken for more than 6 months
2015-11-26 graphics/rubyphoto: Broken for more than 6 months
2015-11-26 german/bsdpaste: Broken for more than 6 months
2015-11-26 audio/amrcoder: Broken for more than 6 months
2015-11-26 sysutils/bashburn: Broken for more than 6 months
2015-11-26 editors/e93: Broken for more than 6 months
2015-11-26 audio/tepsonic: Broken for more than 6 months
2015-11-26 astro/ephem: Broken for more than 6 months
2015-11-26 chinese/cce: Broken for more than 6 months
2015-11-26 graphics/qcread: Broken for more than 6 months
2015-11-26 databases/py-sqlkit: Broken for more than 6 months
2015-11-26 databases/usogres: Broken for more than 6 months
2015-11-26 cad/libgeda: Broken for more than 6 months
2015-11-26 chinese/p5-Lingua-ZH-BPMFConvert: Broken for more than 6 months
2015-11-26 french/alphabet_sounds_fr: Broken for more than 6 months
2015-11-26 deskutils/mrundlg: Broken for more than 6 months
2015-11-26 databases/erlang-mysql: Broken for more than 6 months
2015-11-26 graphics/linux-XnViewMP: Broken for more than 6 months
2015-11-26 deskutils/akamaru: Broken for more than 6 months
2015-11-26 dns/p5-Net-DNS-ZoneCheck: Broken for more than 6 months
2015-11-26 astro/dgpsip: Broken for more than 6 months
2015-11-26 databases/pecl-handlersocket: Broken for more than 6 months
2015-11-26 audio/cymbaline: Broken for more than 6 months
2015-11-26 french/dico: Broken for more than 6 months
2015-11-26 comms/qpage: Broken for more than 6 months
2015-11-26 audio/sonice: Broken for more than 6 months
2015-11-26 cad/geda-symbols: Broken for more than 6 months
2015-11-26 databases/java-mybatis: Broken for more than 6 months
2015-11-26 databases/openbase-jdbc: Broken for more than 6 months
2015-11-27 www/mediawiki119: Please upgrade to mediawiki-1.25
2015-11-28 www/R-cran-Rpad: Unmaintained upstream
genome (e.g. human genome). It has two major components, one for read shorter
than 150bp and the other for longer reads.
WWW: http://sourceforge.net/projects/bio-bwa/
PR: 203158
Submitted by: Jason Bacon <jwbacon@tds.net>
alignments of nucleotide or protein sequences. FastTree can handle alignments
with up to a million of sequences in a reasonable amount of time and memory.
WWW: http://www.microbesonline.org/fasttree/
PR: 203295
Submitted by: Jason Bacon <jwbacon@tds.net>
BCFtools is a set of utilities that manipulate variant calls in the
Variant Call Format (VCF) and its binary counterpart BCF. All
commands work transparently with both VCFs and BCFs, both
uncompressed and BGZF-compressed.
WWW: http://www.htslib.org/
PR: 199747
Submitted by: cartwright@asu.edu
2015-01-01 biology/boinc-simap: Project shutting down, see http://boincsimap.org/boincsimap/forum_thread.php?id=88
2015-01-01 security/openssh-portable-base: Overwrite-base option/port/pkg will be removed. There is no real need for foot-shooting.
2015-01-01 devel/cedet: Fails to build, use Emacs' builtin cedet package instead
2015-01-01 devel/ecb: does not work with newer Emacs versions, use the elpa package instead
SAM, BAM, and CRAM formats, including indexing, variant calling (in conjunction
with bcftools), and a simple alignment viewer.
WWW: http://www.htslib.org/
PR: 195592
Submitted by: Reed A. Cartwright <cartwright@asu.edu>
formats, such as SAM, CRAM, VCF, and BCF, used for high-throughput sequencing
data. It is the core library used by samtools and bcftools.
WWW: http://www.htslib.org/
PR: 195591
Submitted by: Reed A. Cartwright <cartwright@asu.edu>
PR: 190854
Submitted by: Jason Bacon
The Basic Local Alignment Search Tool (BLAST) finds regions of local
similarity between sequences. The program compares nucleotide or protein
sequences to sequence databases and calculates the statistical
significance of matches. BLAST can be used to infer functional and
evolutionary relationships between sequences as well as help identify
members of gene families.
2014-04-16 ports-mgmt/pkgsearch: Upstream disappeared
2014-04-17 science/flounder: Unmaintained since 2002
2014-04-17 security/nbaudit: Unmaintained since 2002
2014-04-17 security/saint: Unmaintained since 2002
2014-04-17 graphics/gozer: Unmaintained since 2002
2014-04-17 misc/pdfmap: Unmaintained since 2002
2014-04-17 devel/showgrammar: Unmaintained since 2002
2014-04-17 biology/libgenome: Unmaintained since 2002
2014-04-17 deskutils/narval: Unmaintained since 2002
2014-04-17 devel/fampp: Unmaintained since 2002
2014-04-17 net-p2p/py-fngrab: Unmaintained since 2002
2014-04-17 misc/wmfirew: Unmaintained since 2002
2014-04-17 x11-wm/e16utils: Unmaintained since 2002
2014-04-17 misc/salias: Unmaintained since 2002
2014-04-17 print/latex2slides: Unmaintained since 2002
2014-04-17 lang/sxm: Unmaintained since 2002
2014-04-17 textproc/pybook: Unmaintained since 2002
2014-04-17 mail/mailcrypt: Unmaintained since 2002
2014-04-17 japanese/elvis: Unmaintained since 2002
2014-04-17 devel/prototype: Unmaintained since 2002
2014-04-17 print/wprint: Unmaintained since 2002
2014-04-17 science/euler: Unmaintained since 2002
2014-04-17 multimedia/gopchop: Unmaintained since 2002
2014-04-17 science/gdis: Unmaintained since 2002
2014-04-17 net/googolplex: Unmaintained since 2002
2014-04-17 lang/logo: Unmaintained since 2002
2014-04-17 textproc/roap: Unmaintained since 2002
2014-04-17 x11-wm/afterstep-i18n: Unmaintained since 2002
2014-04-17 games/yamsweeper: Unmaintained since 2002
2014-04-17 net-mgmt/echolot: Unmaintained since 2002
2014-04-17 security/pam_smb: Unmaintained since 2002
2014-04-18 devel/lua-redis-parser: Broken for more than 6 months
2014-04-18 biology/finchtv: Broken for more than 6 months
2014-04-18 net-im/ari-yahoo: Broken for more than 1 year (http://www.icculus.org/ari-yahoo/)
2014-04-12 net/pvm++: Unmaintained since 2001
2014-04-12 devel/ixlib: Unmaintained since 2001
2014-04-12 mail/althea: Unmaintained since 2001
2014-04-12 graphics/claraocr: Unmaintained since 2001
2014-04-12 graphics/qvplay: Unmaintained since 2001
2014-04-12 print/guitartex: Unmaintained since 2001
2014-04-12 print/pnm2ppa: Unmaintained since 2001
2014-04-12 graphics/opendis: Unmaintained since 2001
2014-04-12 net/gnome-mud: Unmaintained since 2001
2014-04-12 graphics/maverik: Unmaintained since 2001
2014-04-12 biology/rasmol: Unmaintained since 2001
2014-04-12 mail/mail2procmailrc: Unmaintained since 2001
2014-04-12 science/felt: Unmaintained since 2001
2014-04-12 textproc/pardiff: Unmaintained since 2001
2014-04-12 lang/klone: Unmaintained since 2001
2014-04-12 net/rmsg: Unmaintained since 2001
2014-04-12 net/sharity-light: Unmaintained since 2001
2014-04-12 biology/genpak: Unmaintained since 2001
2014-04-12 net/forg: Unmaintained since 2001
2014-04-12 misc/txt2regex: Unmaintained since 2001
2014-04-12 textproc/ipdf: Unmaintained since 2001
2014-04-12 graphics/plotmtv: Unmaintained since 2001
2014-04-12 devel/happydoc: Unmaintained since 2001
2014-04-12 print/cpp2latex: Unmaintained since 2001
2014-04-12 graphics/svg2swf: Unmaintained since 2001
2014-04-12 devel/flick: Unmaintained since 2001
2014-04-12 mail/smail: Unmaintained since 2001
2014-04-12 net/net-http: Unmaintained since 2001
2014-04-12 security/cfv: Unmaintained since 2001
2014-04-12 graphics/camediaplay: Unmaintained since 2001
2014-04-12 math/umatrix: Unmaintained since 2001
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>
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
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
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
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>
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>
