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non port: head/biology/Makefile
SVNWeb

Number of commits found: 109 (showing only 100 on this page)

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Thu, 24 Mar 2016
[ 13:53 amdmi3 ] Original commit 
411785 biology/Makefile
411785 biology/jellyfish
411785 biology/jellyfish/Makefile
411785 biology/jellyfish/distinfo
411785 biology/jellyfish/files
411785 biology/jellyfish/files/patch-include_jellyfish_file__header.hpp
411785 biology/jellyfish/pkg-descr
411785 biology/jellyfish/pkg-plist
Jellyfish is a tool for fast, memory-efficient counting of k-mers in DNA.
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
Wed, 23 Mar 2016
[ 11:22 rakuco ] Original commit 
411698 biology/Makefile
411698 biology/bowtie2
411698 biology/bowtie2/Makefile
411698 biology/bowtie2/distinfo
411698 biology/bowtie2/files
411698 biology/bowtie2/files/patch-Makefile
411698 biology/bowtie2/pkg-descr
411698 biology/bowtie2/pkg-plist
New port: biology/bowtie2.

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>
[ 11:00 rakuco ] Original commit 
411697 biology/Makefile
411697 biology/slclust
411697 biology/slclust/Makefile
411697 biology/slclust/distinfo
411697 biology/slclust/files
411697 biology/slclust/files/patch-include_cmd__line__opts.h
411697 biology/slclust/files/patch-src_Makefile
411697 biology/slclust/pkg-descr
New port: biology/slclust.

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>
Thu, 17 Mar 2016
[ 08:21 wen ] Original commit 
411261 biology/Makefile
411261 biology/trimmomatic
411261 biology/trimmomatic/Makefile
411261 biology/trimmomatic/distinfo
411261 biology/trimmomatic/pkg-descr
411261 biology/trimmomatic/pkg-plist
Trimmomatic performs a variety of useful trimming tasks for illumina
NGS paired-end and single ended data.

WWW: http://www.usadellab.org/cms/?page=trimmomatic

PR:		208044
Submitted by:	bacon4000@gmail.com
Wed, 16 Mar 2016
[ 20:12 pi ] Original commit 
411246 biology/Makefile
411246 biology/p5-transdecoder
411246 biology/p5-transdecoder/Makefile
411246 biology/p5-transdecoder/distinfo
411246 biology/p5-transdecoder/pkg-descr
411246 biology/p5-transdecoder/pkg-plist
New port: biology/p5-transdecoder

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>
Sat, 5 Mar 2016
[ 13:21 rakuco ] Original commit 
410180 biology/Makefile
410180 biology/bowtie
410180 biology/bowtie/Makefile
410180 biology/bowtie/distinfo
410180 biology/bowtie/files
410180 biology/bowtie/files/patch-Makefile
410180 biology/bowtie/pkg-descr
410180 biology/bowtie/pkg-plist
New port: biology/bowtie.

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>
Fri, 26 Feb 2016
[ 17:07 rakuco ] Original commit 
409624 biology/Makefile
409624 biology/vcftools
409624 biology/vcftools/Makefile
409624 biology/vcftools/distinfo
409624 biology/vcftools/pkg-descr
409624 biology/vcftools/pkg-plist
New port: biology/vcftools.

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>
Tue, 19 Jan 2016
[ 08:56 wen ] Original commit 
406676 biology/Makefile
406676 biology/bedtools
406676 biology/bedtools/Makefile
406676 biology/bedtools/distinfo
406676 biology/bedtools/files
406676 biology/bedtools/files/patch-Makefile
406676 biology/bedtools/pkg-descr
406676 biology/bedtools/pkg-plist
The bedtools utilities are a suite of tools for performing a wide range of
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
Sat, 28 Nov 2015
[ 23:08 rene ] Original commit 
402562 MOVED
402562 archivers/Makefile
402562 archivers/wzip
402562 astro/Makefile
402562 astro/aa
402562 astro/dgpsip
402562 astro/ephem
402562 astro/sky2000
402562 astro/wmglobe
402562 audio/Makefile

(Only the first 10 of 114 ports in this commit are shown above. View all ports for this commit)
Remove expired ports:
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
(Only the first 15 lines of the commit message are shown above View all of this commit message)
Fri, 25 Sep 2015
[ 18:39 rm ] Original commit 
397851 biology/Makefile
397851 biology/bwa
397851 biology/bwa/Makefile
397851 biology/bwa/distinfo
397851 biology/bwa/files
397851 biology/bwa/files/patch-Makefile
397851 biology/bwa/files/patch-bwt_lite.c
397851 biology/bwa/files/patch-bwtgap.c
397851 biology/bwa/files/patch-bwtgap.h
397851 biology/bwa/pkg-descr
BWA is a program for aligning sequencing reads against a large reference
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>
[ 18:37 rm ] Original commit 
397850 biology/Makefile
397850 biology/cdbfasta
397850 biology/cdbfasta/Makefile
397850 biology/cdbfasta/distinfo
397850 biology/cdbfasta/files
397850 biology/cdbfasta/files/patch-Makefile
397850 biology/cdbfasta/pkg-descr
Fast indexing and retrieval of FASTA records from flat file data bases.

WWW: http://sourceforge.net/projects/cdbfasta/

PR:		203233
Submitted by:	Jason Bacon <jwbacon@tds.net>
[ 18:35 rm ] Original commit 
397849 biology/Makefile
397849 biology/fastool
397849 biology/fastool/Makefile
397849 biology/fastool/distinfo
397849 biology/fastool/pkg-descr
Simple and quick FastQ and FastA tool for file reading and conversion.

WWW: https://github.com/fstrozzi/Fastool

PR:		203293
Submitted by:	Jason Bacon <jwbacon@tds.net>
[ 18:34 rm ] Original commit 
397848 biology/Makefile
397848 biology/fasttree
397848 biology/fasttree/Makefile
397848 biology/fasttree/distinfo
397848 biology/fasttree/pkg-descr
FastTree infers approximately-maximum-likelihood phylogenetic trees from
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>
[ 18:33 rm ] Original commit 
397847 biology/Makefile
397847 biology/fastx-toolkit
397847 biology/fastx-toolkit/Makefile
397847 biology/fastx-toolkit/distinfo
397847 biology/fastx-toolkit/pkg-descr
397847 biology/fastx-toolkit/pkg-plist
The FASTX-Toolkit is a collection of command line tools for Short-Reads
FASTA/FASTQ files preprocessing.

WWW: http://hannonlab.cshl.edu/fastx_toolkit/

PR:		203318
Submitted by:	Jason Bacon <jwbacon@tds.net>
[ 18:31 rm ] Original commit 
397846 biology/Makefile
397846 biology/libgtextutils
397846 biology/libgtextutils/Makefile
397846 biology/libgtextutils/distinfo
397846 biology/libgtextutils/pkg-descr
397846 biology/libgtextutils/pkg-plist
Gordon's text utilities.

WWW: https://github.com/agordon/libgtextutils

PR:		203309
Submitted by:	Jason Bacon <jwbacon@tds.net>
Sat, 19 Sep 2015
[ 11:16 wen ] Original commit 
397318 biology/Makefile
397318 biology/cd-hit
397318 biology/cd-hit/Makefile
397318 biology/cd-hit/distinfo
397318 biology/cd-hit/pkg-descr
397318 biology/cd-hit/pkg-plist
CD-HIT is a very widely used program for clustering and comparing protein or
nucleotide sequences.

WWW: http://weizhong-lab.ucsd.edu/cd-hit/

PR:		203183
Submitted by:	jwbacon@tds.net
Fri, 5 Jun 2015
[ 21:01 pi ] Original commit 
388638 biology/Makefile
388638 biology/bcftools
388638 biology/bcftools/Makefile
388638 biology/bcftools/distinfo
388638 biology/bcftools/files
388638 biology/bcftools/files/patch-Makefile
388638 biology/bcftools/files/patch-plugins_fixploidy.mk
388638 biology/bcftools/files/patch-plugins_vcf2sex.mk
388638 biology/bcftools/files/patch-prob1.c
388638 biology/bcftools/files/pkg-message.in

(Only the first 10 of 12 ports in this commit are shown above. View all ports for this commit)
New port: biology/bcftools

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
Thu, 1 Jan 2015
[ 01:13 rene ] Original commit 
375913 MOVED
375913 biology/Makefile
375913 biology/boinc-simap
375913 devel/Makefile
375913 devel/cedet
375913 devel/ecb
375913 security/Makefile
375913 security/openssh-portable-base
Remove expired ports:
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
Tue, 30 Dec 2014
[ 20:03 grembo ] Original commit 
375848 MOVED
375848 biology/Makefile
375848 biology/ncbi-blast
375848 biology/ncbi-blast+
375848 biology/ncbi-blast+/Makefile
Rename biology/ncbi-blast to biology/ncbi-blast+

Approved by:	mentors (implicit)
Mon, 15 Dec 2014
[ 21:59 pawel ] Original commit 
374767 biology/Makefile
374767 biology/samtools
374767 biology/samtools/Makefile
374767 biology/samtools/distinfo
374767 biology/samtools/files
374767 biology/samtools/files/patch-Makefile
374767 biology/samtools/files/patch-errmod.c
374767 biology/samtools/files/pkg-message.in
374767 biology/samtools/pkg-descr
374767 biology/samtools/pkg-plist
Samtools implements various utilities for post-processing alignments in the
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>
Sun, 14 Dec 2014
[ 22:35 pawel ] Original commit 
374729 biology/Makefile
374729 biology/htslib
374729 biology/htslib/Makefile
374729 biology/htslib/distinfo
374729 biology/htslib/files
374729 biology/htslib/files/patch-Makefile
374729 biology/htslib/pkg-descr
374729 biology/htslib/pkg-plist
HTSlib is an implementation of a unified C library for accessing common file
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>
Mon, 6 Oct 2014
[ 20:16 marino ] Original commit 
370220 biology/Makefile
370220 biology/ncbi-blast
370220 biology/ncbi-blast/Makefile
370220 biology/ncbi-blast/distinfo
370220 biology/ncbi-blast/pkg-descr
370220 biology/ncbi-blast/pkg-plist
Add new port biology/ncbi-blast

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.
Tue, 2 Sep 2014
[ 12:45 bapt ] Original commit 
366995 MOVED
366995 biology/Makefile
366995 biology/phd2fasta
366995 databases/Makefile
366995 databases/kumofs
366995 devel/Makefile
366995 devel/lxr
366995 devel/scsh-install-lib
366995 games/Makefile
366995 games/qix

(Only the first 10 of 15 ports in this commit are shown above. View all ports for this commit)
Second run at cleaning out non staged ports without pending PR
Mon, 1 Sep 2014
[ 11:37 bapt ] Original commit 
366862 MOVED
366862 benchmarks/spec-sfs
366862 biology/Makefile
366862 biology/blast
366862 biology/embassy
366862 biology/pymol
Remove non staged ports without pending PR from b*
Fri, 18 Apr 2014
[ 11:17 rene ] Original commit 
351531 MOVED
351531 biology/Makefile
351531 biology/finchtv
351531 biology/libgenome
351531 deskutils/Makefile
351531 deskutils/narval
351531 devel/Makefile
351531 devel/fampp
351531 devel/lua-redis-parser
351531 devel/prototype

(Only the first 10 of 55 ports in this commit are shown above. View all ports for this commit)
Remove expired ports:
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
(Only the first 15 lines of the commit message are shown above View all of this commit message)
Sun, 13 Apr 2014
[ 10:55 rene ] Original commit 
351202 MOVED
351202 biology/Makefile
351202 biology/genpak
351202 biology/rasmol
351202 devel/Makefile
351202 devel/flick
351202 devel/happydoc
351202 devel/ixlib
351202 graphics/Makefile
351202 graphics/camediaplay

(Only the first 10 of 44 ports in this commit are shown above. View all ports for this commit)
Remove expired ports:
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
(Only the first 15 lines of the commit message are shown above View all of this commit message)
Sun, 10 Nov 2013
[ 11:01 wg ] Original commit 
333374 MOVED
333374 biology/Makefile
333374 biology/dotter
333374 biology/seqtools
333374 biology/seqtools/Makefile
333374 biology/seqtools/distinfo
333374 biology/seqtools/pkg-descr
333374 biology/seqtools/pkg-plist
biology/seqtools: Tools for visualising sequence alignments

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>
Thu, 29 Aug 2013
[ 02:28 bdrewery ] Original commit 
325558 audio/Makefile
325558 biology/Makefile
325558 databases/Makefile
325558 deskutils/Makefile
325558 devel/Makefile
325558 editors/Makefile
325558 games/Makefile
325558 irc/Makefile
325558 math/Makefile
325558 net/Makefile

(Only the first 10 of 13 ports in this commit are shown above. View all ports for this commit)
- Disconnect ports removed in r325546
Fri, 26 Jul 2013
[ 19:19 rene ] Original commit 
323748 CHANGES
323748 KNOBS
323748 MOVED
323748 Mk/bsd.kde.mk
323748 Mk/bsd.qt.mk
323748 accessibility/Makefile
323748 accessibility/kdeaccessibility
323748 arabic/Makefile
323748 arabic/kde3-i18n
323748 archivers/Makefile

(Only the first 10 of 435 ports in this commit are shown above. View all ports for this commit)
KDE3 and QT3 expired on 2013-07-01, remove these ports.
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
Sat, 23 Feb 2013
[ 04:50 danfe ] Original commit 
312798 biology/Makefile
312798 biology/ugene
312798 biology/ugene/Makefile
312798 biology/ugene/distinfo
312798 biology/ugene/files
312798 biology/ugene/files/patch-src-corelibs-U2Private-src-CrashHandler.cpp
312798 biology/ugene/pkg-descr
312798 biology/ugene/pkg-plist
Add Unipro UGENE, a free open-source crowss-platform bioinformatics software.

PR:		ports/173387
Submitted by:	Hannes Hauswedell
Wed, 28 Nov 2012
[ 09:05 bapt ] Original commit 
307892 MOVED
307892 benchmarks/Makefile
307892 benchmarks/gsbench
307892 benchmarks/xengine
307892 biology/Makefile
307892 biology/belvu
307892 multimedia/Makefile
307892 multimedia/kaffeine-mozilla
307892 net/Makefile
307892 net/tryst

(Only the first 10 of 13 ports in this commit are shown above. View all ports for this commit)
2012-11-26 benchmarks/gsbench: No more public distfiles
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
Thu, 25 Oct 2012
[ 23:05 bapt ] Original commit 
306411 LEGAL
306411 MOVED
306411 biology/Makefile
306411 biology/dna-qc
306411 chinese/Makefile
306411 chinese/dfsongsd
306411 chinese/mingunittf
306411 chinese/stardict-dict-zh_CN
306411 chinese/stardict-dict-zh_TW
306411 chinese/wangttf
2012-10-20 chinese/wangttf: No more public distfiles
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
Thu, 27 Sep 2012
[ 09:59 makc ] Original commit 
304954 biology/Makefile
304954 biology/plink
304954 biology/plink/Makefile
304954 biology/plink/distinfo
304954 biology/plink/files
304954 biology/plink/files/patch-Makefile
304954 biology/plink/pkg-descr
304954 biology/plinkseq
304954 biology/plinkseq/Makefile
304954 biology/plinkseq/distinfo

(Only the first 10 of 12 ports in this commit are shown above. View all ports for this commit)
Add new ports biology/plink [1] and biology/plinkseq [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>
Wed, 6 Jun 2012
[ 17:51 amdmi3 ] Original commit 
1.121 biology/Makefile
1.1 biology/seqan/Makefile
1.1 biology/seqan/distinfo
1.1 biology/seqan/files/patch-cmake-CMakeLists.txt
1.1 biology/seqan/files/patch-cmake-apps-CMakeLists.txt
1.1 biology/seqan/files/pkg-message.in
1.1 biology/seqan/pkg-descr
1.1 biology/seqan/pkg-plist
SeqAn is an open source C++ library of efficient algorithms
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>
Mon, 1 Aug 2011
[ 04:29 bapt ] Original commit 
1.666 LEGAL
1.2539 MOVED
1.73 benchmarks/Makefile
1.18 benchmarks/rawio/Makefile
1.11 benchmarks/rawio/distinfo
1.6 benchmarks/rawio/files/patch-ad
1.2 benchmarks/rawio/pkg-descr
1.15 benchmarks/tmetric/Makefile
1.11 benchmarks/tmetric/distinfo
1.5 benchmarks/tmetric/pkg-descr

(Only the first 10 of 151 ports in this commit are shown above. View all ports for this commit)
Bye bye abandonwares (part 2)

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
Fri, 22 Apr 2011
[ 08:51 wen ] Original commit 
1.119 biology/Makefile
1.1 biology/p5-Bio-GFF3/Makefile
1.1 biology/p5-Bio-GFF3/distinfo
1.1 biology/p5-Bio-GFF3/pkg-descr
1.1 biology/p5-Bio-GFF3/pkg-plist
Bio::GFF3 are low-level, fast functions for parsing GFF version 3 files.
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/
Mon, 1 Mar 2010
[ 09:16 wen ] Original commit 
1.118 biology/Makefile
1.1 biology/p5-Bio-Das-Lite/Makefile
1.1 biology/p5-Bio-Das-Lite/distinfo
1.1 biology/p5-Bio-Das-Lite/pkg-descr
1.1 biology/p5-Bio-Das-Lite/pkg-plist
p5-Bio-Das-Lite is an implementation of a client for the DAS protocol (XML
over HTTP primarily for biological-data).

WWW: http://search.cpan.org/dist/Bio-Das-Lite/

Feature safe:   yes
Tue, 29 Dec 2009
[ 13:39 wen ] Original commit 
1.117 biology/Makefile
1.1 biology/python-nexus/Makefile
1.1 biology/python-nexus/distinfo
1.1 biology/python-nexus/pkg-descr
1.1 biology/python-nexus/pkg-plist
python-nexus is a generic nexus (phylogenetics) file format(.nex, .trees)
reader for python.

WWW:    http://simon.net.nz/articles/python-nexus
Wed, 18 Nov 2009
[ 05:53 wen ] Original commit 
1.116 biology/Makefile
1.1 biology/pyfasta/Makefile
1.1 biology/pyfasta/distinfo
1.1 biology/pyfasta/pkg-descr
1.1 biology/pyfasta/pkg-plist
pyfasta is a python module for fast, memory-efficient, pythonic
access to fasta sequence files.

WWW:    http://bitbucket.org/brentp/biostuff/src/
Sat, 7 Nov 2009
[ 01:23 amdmi3 ] Original commit 
1.115 biology/Makefile
1.1 biology/velvet/Makefile
1.1 biology/velvet/distinfo
1.1 biology/velvet/files/patch-Makefile
1.1 biology/velvet/files/patch-contrib-VelvetOptimiser-VelvetOptimiser.pl
1.1 biology/velvet/files/patch-src-run.c
1.1 biology/velvet/pkg-descr
Velvet is a de novo genomic assembler specially designed for short read
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>
Fri, 28 Aug 2009
[ 23:36 miwi ] Original commit 
1.114 biology/Makefile
1.1 biology/p5-Bio-SCF/Makefile
1.1 biology/p5-Bio-SCF/distinfo
1.1 biology/p5-Bio-SCF/pkg-descr
1.1 biology/p5-Bio-SCF/pkg-plist
Bio::SCF module allows you to read and update (in a restricted
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>
[ 23:34 miwi ] Original commit 
1.113 biology/Makefile
1.1 biology/iolib/Makefile
1.1 biology/iolib/distinfo
1.1 biology/iolib/pkg-descr
1.1 biology/iolib/pkg-plist
Io_lib is a library of file reading and writing code to provide a
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>
Sat, 22 Aug 2009
[ 20:39 miwi ] Original commit 
1.112 biology/Makefile
1.1 biology/p5-Bio-NEXUS/Makefile
1.1 biology/p5-Bio-NEXUS/distinfo
1.1 biology/p5-Bio-NEXUS/pkg-descr
1.1 biology/p5-Bio-NEXUS/pkg-plist
Bio::NEXUS package provides an object-oriented, Perl-based
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>
Tue, 21 Jul 2009
[ 01:10 amdmi3 ] Original commit 
1.111 biology/Makefile
1.1 biology/phyml/Makefile
1.1 biology/phyml/distinfo
1.1 biology/phyml/files/patch-src-configure
1.1 biology/phyml/files/patch-src-configure.ac
1.1 biology/phyml/pkg-descr
PhyML is a software that estimates maximum likelihood phylogenies from
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>
Wed, 1 Jul 2009
[ 09:03 miwi ] Original commit 
1.110 biology/Makefile
1.1 biology/p5-Bio-MAGETAB/Makefile
1.1 biology/p5-Bio-MAGETAB/distinfo
1.1 biology/p5-Bio-MAGETAB/pkg-descr
1.1 biology/p5-Bio-MAGETAB/pkg-plist
p5-Bio-MAGETAB contains the core MAGE-TAB Utilities Perl modules. This
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>
Mon, 22 Jun 2009
[ 12:46 miwi ] Original commit 
1.109 biology/Makefile
1.1 biology/pycogent/Makefile
1.1 biology/pycogent/distinfo
1.1 biology/pycogent/pkg-descr
1.1 biology/pycogent/pkg-plist
PyCogent is a software library for genomic biology. It is a fully integrated
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>
Mon, 8 Jun 2009
[ 23:49 jasone ] Original commit 
1.108 biology/Makefile
1.1 biology/crux/Makefile
1.1 biology/crux/distinfo
1.1 biology/crux/pkg-descr
1.1 biology/crux/pkg-plist
Add the biology/crux port.
Fri, 5 Jun 2009
[ 20:38 miwi ] Original commit 
1.1873 MOVED
1.107 biology/Makefile
1.17 biology/p5-bioperl-devel/Makefile
1.5 biology/p5-bioperl-devel/distinfo
1.2 biology/p5-bioperl-devel/files/patch-Build.PL
1.2 biology/p5-bioperl-devel/files/patch-ModuleBuildBioperl.pm
1.4 biology/p5-bioperl-devel/pkg-descr
1.6 biology/p5-bioperl-devel/pkg-plist
1.6 biology/p5-bioperl-run-devel/Makefile
1.2 biology/p5-bioperl-run-devel/distinfo

(Only the first 10 of 30 ports in this commit are shown above. View all ports for this commit)
2009-05-31 biology/p5-bioperl-devel: no longer under development
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
Thu, 28 May 2009
[ 23:36 miwi ] Original commit 
1.106 biology/Makefile
1.1 biology/libsbml/Makefile
1.1 biology/libsbml/distinfo
1.1 biology/libsbml/files/patch-Makefile.in
1.1 biology/libsbml/pkg-descr
1.1 biology/libsbml/pkg-plist
LibSBML is an open-source programming library to help you read, write,
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>
Thu, 2 Apr 2009
[ 18:24 miwi ] Original commit 
1.105 biology/Makefile
1.1 biology/p5-Bio-Glite/Makefile
1.1 biology/p5-Bio-Glite/distinfo
1.1 biology/p5-Bio-Glite/pkg-descr
1.1 biology/p5-Bio-Glite/pkg-plist
Bio::Glite is an interface to G-language Genome Analysis Environment
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>
Tue, 10 Mar 2009
[ 18:50 miwi ] Original commit 
1.104 biology/Makefile
1.1 biology/p5-Bio-Graphics/Makefile
1.1 biology/p5-Bio-Graphics/distinfo
1.1 biology/p5-Bio-Graphics/pkg-descr
1.1 biology/p5-Bio-Graphics/pkg-plist
p5-Bio-Graphics is a simple GD-based renderer (diagram drawer)
for DNA and protein sequences.

WWW: http://search.cpan.org/dist/Bio-Graphics/

PR:             ports/132088
Submitted by:   Wen Heping <wenheping at gmail.com>
Thu, 24 Jul 2008
[ 12:17 pav ] Original commit 
1.103 biology/Makefile
1.23 biology/nab/Makefile
1.12 biology/nab/distinfo
1.9 biology/nab/files/config.h
1.6 biology/nab/files/patch-Makefile
1.2 biology/nab/files/patch-configure
1.2 biology/nab/files/patch-reslib:conf.lib
1.2 biology/nab/files/patch-src:wc_helix.nab
1.4 biology/nab/files/patch-src_Makefile
1.2 biology/nab/files/patch-src_cgen.c

(Only the first 10 of 15 ports in this commit are shown above. View all ports for this commit)
- Delete biology/nab port after being marked DEPRECATED for three months

PR:             ports/125891
Submitted by:   M. L. Dodson <mldodson@comcast.net> (maintainer)
Sat, 21 Jun 2008
[ 00:01 lippe ] Original commit 
1.102 biology/Makefile
1.1 biology/ssaha/Makefile
1.1 biology/ssaha/distinfo
1.1 biology/ssaha/files/patch-GlobalDefinitions.cpp
1.1 biology/ssaha/files/patch-GlobalDefinitions.h
1.1 biology/ssaha/files/patch-HashTable.cpp
1.1 biology/ssaha/files/patch-HashTableGeneric.cpp
1.1 biology/ssaha/files/patch-HashTablePacked.cpp
1.1 biology/ssaha/files/patch-HashTablePacked.h
1.1 biology/ssaha/files/patch-HashTableTranslated.cpp

(Only the first 10 of 36 ports in this commit are shown above. View all ports for this commit)
SSAHA is a software tool for very fast matching and alignment of DNA
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)
Sat, 24 May 2008
[ 07:04 edwin ] Original commit 
1.101 biology/Makefile
1.1 biology/phred/Makefile
1.1 biology/phred/distinfo
1.1 biology/phred/files/patch-Makefile
1.1 biology/phred/pkg-descr
New port: biology/consed viewing and editing workbench for sequence
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>
[ 07:03 edwin ] Original commit 
1.100 biology/Makefile
1.1 biology/phrap/Makefile
1.1 biology/phrap/distinfo
1.1 biology/phrap/files/patch-makefile
1.1 biology/phrap/pkg-descr
New port: biology/consed viewing and editing workbench for sequence
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>
[ 07:01 edwin ] Original commit 
1.99 biology/Makefile
1.1 biology/phd2fasta/Makefile
1.1 biology/phd2fasta/distinfo
1.1 biology/phd2fasta/files/patch-Makefile
1.1 biology/phd2fasta/pkg-descr
New port: biology/consed viewing and editing workbench for sequence
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>
[ 07:00 edwin ] Original commit 
1.98 biology/Makefile
1.1 biology/consed/Makefile
1.1 biology/consed/distinfo
1.1 biology/consed/files/patch-misc_mktrace.c
1.1 biology/consed/files/patch-scripts_addReads2Consed.perl
1.1 biology/consed/files/patch-scripts_determineReadTypes.perl
1.1 biology/consed/files/patch-scripts_phredPhrap
1.1 biology/consed/pkg-descr
1.1 biology/consed/pkg-plist.examples
New port: biology/consed viewing and editing workbench for sequence
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>
Wed, 14 May 2008
[ 14:07 pav ] Original commit 
1.97 biology/Makefile
1.1 biology/njplot/Makefile
1.1 biology/njplot/distinfo
1.1 biology/njplot/files/patch-makefile
1.1 biology/njplot/pkg-descr
NJplot is a tree drawing program able to draw any phylogenetic tree expressed
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>
[ 13:51 pav ] Original commit 
1.96 biology/Makefile
1.1 biology/muscle/Makefile
1.1 biology/muscle/distinfo
1.1 biology/muscle/files/patch-Makefile
1.1 biology/muscle/files/patch-globalslinux.cpp
1.1 biology/muscle/files/patch-intmath.cpp
1.1 biology/muscle/pkg-descr
MUSCLE is multiple alignment software for protein and nucleotide sequences.
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>
Sun, 6 Apr 2008
[ 04:49 rafan ] Original commit 
1.95 biology/Makefile
1.1 biology/mapm3/Makefile
1.1 biology/mapm3/distinfo
1.1 biology/mapm3/files/patch-Makefile
1.1 biology/mapm3/files/patch-lib-iolib.c
1.1 biology/mapm3/files/patch-lib-iolib.h
1.1 biology/mapm3/files/patch-lib-makehelp.c
1.1 biology/mapm3/files/patch-lib-shell.c
1.1 biology/mapm3/files/patch-lib-syscode.c
1.1 biology/mapm3/files/patch-lib-system.h

(Only the first 10 of 28 ports in this commit are shown above. View all ports for this commit)
MAPMAKER/EXP is a linkage analysis package designed to help construct primary
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>
Sat, 15 Dec 2007
[ 15:13 miwi ] Original commit 
1.94 biology/Makefile
1.1 biology/mrbayes/Makefile
1.1 biology/mrbayes/distinfo
1.1 biology/mrbayes/files/patch-Makefile
1.1 biology/mrbayes/pkg-descr
MrBayes is a program for the Bayesian estimation of phylogeny.

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
Fri, 14 Dec 2007
[ 20:54 miwi ] Original commit 
1.93 biology/Makefile
1.1 biology/mummer/Makefile
1.1 biology/mummer/distinfo
1.1 biology/mummer/pkg-descr
1.1 biology/mummer/pkg-plist
MUMmer is a modular system for the rapid whole genome alignment of finished
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
Fri, 5 Oct 2007
[ 23:33 sat ] Original commit 
1.118 astro/Makefile
1.904 audio/Makefile
1.92 biology/Makefile
1.259 chinese/Makefile
1.644 databases/Makefile
1.2902 devel/Makefile
1.84 dns/Makefile
1.236 emulators/Makefile
1.1153 games/Makefile
1.1108 graphics/Makefile

(Only the first 10 of 22 ports in this commit are shown above. View all ports for this commit)
- Sort category Makefiles

Inspired by:    Jason Harris <jharris@widomaker.com>
Howto:          http://twiki.cenkes.org/Cenkes/SortingCategoryMakefiles
Thu, 25 Jan 2007
[ 11:25 vd ] Original commit 
1.17213 /CVSROOT/modules
1.1263 MOVED
1.91 biology/Makefile
1.6 biology/coalesce/Makefile
1.5 biology/coalesce/distinfo
1.2 biology/coalesce/files/patch-Makefile
1.2 biology/coalesce/pkg-descr
1.3 biology/coalesce/pkg-plist
Remove expired leaf port:
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.
Sat, 30 Dec 2006
[ 09:20 dinoex ] Original commit 
1.90 biology/Makefile
1.1 biology/biococoa/Makefile
1.1 biology/biococoa/distinfo
1.1 biology/biococoa/pkg-descr
1.1 biology/biococoa/pkg-plist
The BioCocoa framework provides developers with the opportunity to add
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/
Thu, 9 Nov 2006
[ 20:16 dinoex ] Original commit 
1.89 biology/Makefile
1.1 biology/adun/Makefile
1.1 biology/adun/distinfo
1.1 biology/adun/files/patch-AdunLinkedList.m
1.1 biology/adun/files/patch-AdunMemoryManager.h
1.1 biology/adun/files/patch-AdunMemoryManager.m
1.1 biology/adun/files/patch-GNUmakefile
1.1 biology/adun/files/patch-main.m
1.1 biology/adun/pkg-descr
1.1 biology/adun/pkg-plist
Adun is a new extendible molecular simulation program that also
includes data management and analysis capabilities.

WWW: http://diana.imim.es/Adun
Submitted by:   Gürkan Sengün
Reviewed by:    dinoex
Fri, 29 Sep 2006
[ 04:05 clsung ] Original commit 
1.88 biology/Makefile
1.1 biology/gmap/Makefile
1.1 biology/gmap/distinfo
1.1 biology/gmap/files/extra-patch-src-genome.c
1.1 biology/gmap/files/extra-patch-src-indexdb.c
1.1 biology/gmap/files/patch-configure
1.1 biology/gmap/pkg-descr
1.1 biology/gmap/pkg-plist
Add gmap 2006.04.21, a Genomic Mapping and Alignment Program for mRNA
and EST Sequences.

PR:             ports/103651
Submitted by:   Bob Zimmermann <rpz at cse.wustl.edu>
Mon, 28 Aug 2006
[ 22:33 pav ] Original commit 
1.87 biology/Makefile
1.1 biology/linux-foldingathome/Makefile
1.1 biology/linux-foldingathome/distinfo
1.1 biology/linux-foldingathome/pkg-descr
1.1 biology/linux-foldingathome/scripts/FoldingAtHome
Folding@Home is a distributed computing project -- people from through out the
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>
Mon, 19 Jun 2006
[ 20:32 pav ] Original commit 
1.86 biology/Makefile
1.1 biology/boinc-simap/Makefile
1.1 biology/boinc-simap/distinfo
1.1 biology/boinc-simap/files/app_info.xml.in
1.1 biology/boinc-simap/pkg-descr
1.1 biology/boinc-simap/pkg-message
1.1 biology/boinc-simap/pkg-plist
SIMAP (Similarity Matrix of Proteins) is a public database of pre-calculated
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/
Sat, 13 May 2006
[ 16:48 aaron ] Original commit 
1.85 biology/Makefile
1.1 biology/p5-Bio-Phylo/Makefile
1.1 biology/p5-Bio-Phylo/distinfo
1.1 biology/p5-Bio-Phylo/pkg-descr
1.1 biology/p5-Bio-Phylo/pkg-plist
Adding port biology/p5-Bio-Phylo, Phylogenetic analysis using perl.

Approved by:    tobez (implicit)
Fri, 5 May 2006
[ 20:09 ehaupt ] Original commit 
1.84 biology/Makefile
1.1 biology/protomol/Makefile
1.1 biology/protomol/distinfo
1.1 biology/protomol/pkg-descr
1.1 biology/protomol/pkg-plist
Add protomol 2.0.3, OO, component based, framework for molecular
dynamics (MD) simulations.

PR:             95123
Submitted by:   Sangwoo Shim <sangwoos@gmail.com>
Tue, 2 May 2006
[ 21:31 garga ] Original commit 
1.83 biology/Makefile
1.1 biology/p5-bioperl-run-devel/Makefile
1.1 biology/p5-bioperl-run-devel/distinfo
1.1 biology/p5-bioperl-run-devel/pkg-descr
1.1 biology/p5-bioperl-run-devel/pkg-plist
Bioperl-run contain modules that provides a PERL interface to various
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>
[ 21:30 garga ] Original commit 
1.82 biology/Makefile
1.1 biology/p5-bioperl-run/Makefile
1.1 biology/p5-bioperl-run/distinfo
1.1 biology/p5-bioperl-run/pkg-descr
1.1 biology/p5-bioperl-run/pkg-plist
Bioperl-run contain modules that provides a PERL interface to various
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>
Thu, 16 Mar 2006
[ 22:31 garga ] Original commit 
1.81 biology/Makefile
1.1 biology/lagan/Makefile
1.1 biology/lagan/distinfo
1.1 biology/lagan/files/pkg-message.in
1.1 biology/lagan/pkg-descr
1.1 biology/lagan/pkg-plist
Add lagan 1.2, efficient tools for large-scale multiple alignments of
genomic DNA.

PR:             ports/93058
Submitted by:   Fernan Aguero <fernan@iib.unsam.edu.ar>
Wed, 15 Mar 2006
[ 10:41 garga ] Original commit 
1.80 biology/Makefile
1.1 biology/mafft/Makefile
1.1 biology/mafft/distinfo
1.1 biology/mafft/files/patch-Makefile
1.1 biology/mafft/pkg-descr
1.1 biology/mafft/pkg-plist
Add mafft 5.734, multiple sequence alignments based on fast Fourier
transform.

PR:             ports/93059
Submitted by:   Fernan Aguero <fernan@iib.unsam.edu.ar>
[ 10:35 garga ] Original commit 
1.79 biology/Makefile
1.1 biology/dotter/Makefile
1.1 biology/dotter/distinfo
1.1 biology/dotter/pkg-descr
Add dotter 20021204 # last modified date in FTP server, a viewer for
multiple sequence alignments.

PR:             ports/93055
Submitted by:   Fernan Aguero <fernan@iib.unsam.edu.ar>
[ 10:26 garga ] Original commit 
1.78 biology/Makefile
1.1 biology/blat/Makefile
1.1 biology/blat/distinfo
1.1 biology/blat/files/pkg-message.in
1.1 biology/blat/pkg-descr
1.1 biology/blat/pkg-plist
Add blat 33, a fast tool for local sequence similarity searches.

PR:             ports/93060
Submitted by:   Fernan Aguero <fernan@iib.unsam.edu.ar>
[ 10:24 garga ] Original commit 
1.77 biology/Makefile
1.1 biology/belvu/Makefile
1.1 biology/belvu/distinfo
1.1 biology/belvu/pkg-descr
Add belvu 2.29, a viewer for multiple sequence alignments.

PR:             ports/93056
Submitted by:   Fernan Aguero <fernan@iib.unsam.edu.ar>
Mon, 13 Feb 2006
[ 09:42 hq ] Original commit 
1.76 biology/Makefile
1.1 biology/jalview/Makefile
1.1 biology/jalview/distinfo
1.1 biology/jalview/files/jalview.sh.in
1.1 biology/jalview/files/patch-build.xml
1.1 biology/jalview/pkg-descr
1.1 biology/jalview/pkg-plist
Jalview is a multiple alignment editor written in Java. It is used widely in a
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>
Thu, 19 Jan 2006
[ 19:47 danfe ] Original commit 
1.882 MOVED
1.75 biology/Makefile
1.10 biology/chemeq/Makefile
1.5 biology/chemeq/distinfo
1.3 biology/chemeq/pkg-descr
1.5 biology/chemeq/pkg-plist
- Resurrect, update to version 1.5 (literally 1.50 since I wanted to avoid
  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
Sat, 14 Jan 2006
[ 21:15 pav ] Original commit 
1.875 MOVED
1.97 astro/Makefile
1.11 astro/gkrellmearth/Makefile
1.3 astro/gkrellmearth/distinfo
1.3 astro/gkrellmearth/files/patch-Makefile
1.3 astro/gkrellmearth/pkg-descr
1.690 audio/Makefile
1.11 audio/mziq/Makefile
1.8 audio/mziq/distinfo
1.3 audio/mziq/pkg-descr

(Only the first 10 of 123 ports in this commit are shown above. View all ports for this commit)
- Remove expired ports
Fri, 2 Dec 2005
[ 21:40 barner ] Original commit 
1.13782 /CVSROOT/modules
1.73 biology/Makefile
1.7 biology/p5-bioperl-devel/Makefile
1.3 biology/p5-bioperl-devel/distinfo
1.1 biology/p5-bioperl-devel/files/patch-Makefile.PL
1.3 biology/p5-bioperl-devel/pkg-descr
1.3 biology/p5-bioperl-devel/pkg-plist
- Re-add p5-bioperl-devel, development version of biology/p5-bioperl
  (A collection of Perl modules for bioinformatics)

PR:             ports/89497
Submitted by:   Mauricio Herrera Cuadra <arareko@yahoo.com>
Sat, 5 Nov 2005
[ 09:07 kris ] Original commit 
1.672 audio/Makefile
1.10 audio/musicbox/Makefile
1.5 audio/musicbox/distinfo
1.4 audio/musicbox/files/patch-ListView.cpp
1.2 audio/musicbox/files/patch-ListView.h
1.4 audio/musicbox/files/patch-Makefile
1.4 audio/musicbox/files/patch-MultiListBox.h
1.4 audio/musicbox/files/patch-player.cpp
1.4 audio/musicbox/files/patch-qktstreelist.cpp
1.5 audio/musicbox/pkg-descr

(Only the first 10 of 583 ports in this commit are shown above. View all ports for this commit)
Remove expired ports
Sat, 15 Oct 2005
[ 20:09 ehaupt ] Original commit 
1.71 biology/Makefile
1.1 biology/p5-Bio-ASN1-EntrezGene/Makefile
1.1 biology/p5-Bio-ASN1-EntrezGene/distinfo
1.1 biology/p5-Bio-ASN1-EntrezGene/pkg-descr
1.1 biology/p5-Bio-ASN1-EntrezGene/pkg-plist
Add p5-Bio-ASN1-EntrezGene, a Regular expression-based Perl Parser for
NCBI Entrez Gene.

PR:             87423
Submitted by:   Mauricio Herrera Cuadra <mauricio@arareko.net>
Approved by:    novel (mentor) (implicit)
Thu, 1 Sep 2005
[ 13:09 garga ] Original commit 
1.70 biology/Makefile
1.1 biology/p5-Bio-Das/Makefile
1.1 biology/p5-Bio-Das/distinfo
1.1 biology/p5-Bio-Das/pkg-descr
1.1 biology/p5-Bio-Das/pkg-plist
Add p5-Bio-Das 1.02, client-side library for Distributed Genome
Annotation System.

PR:             ports/76379
Submitted by:   Razi Khaja <razi@genet.sickkids.on.ca>
Sat, 12 Mar 2005
[ 08:07 sem ] Original commit 
1.649 MOVED
1.69 biology/Makefile
1.5 biology/act/Makefile
1.4 biology/act/distinfo
1.2 biology/act/pkg-descr
1.3 biology/act/pkg-plist
- biology/act is redundant after biology/artemis update

PR:             ports/76217
Submitted by:   Fernan Aguero <fernan@iib.unsam.edu.ar>
Approved by:    maintainer timeout (2 monthes)
Fri, 11 Mar 2005
[ 21:16 thierry ] Original commit 
1.68 biology/Makefile
1.1 biology/finchtv/Makefile
1.1 biology/finchtv/distinfo
1.1 biology/finchtv/files/pkg-message.in
1.1 biology/finchtv/pkg-descr
1.1 biology/finchtv/pkg-plist
Add finchtv 1.3.0, a chromatogram trace viewer.

PR:             70271
Submitted by:   Fernan Aguero <fernan (at) iib.unsam.edu.ar>
Fri, 18 Feb 2005
[ 23:44 kris ] Original commit 
1.591 audio/Makefile
1.10 audio/xmms-arts/Makefile
1.4 audio/xmms-arts/distinfo
1.2 audio/xmms-arts/files/patch-Makefile.in
1.2 audio/xmms-arts/files/patch-init.c
1.4 audio/xmms-arts/pkg-descr
1.4 audio/xmms-arts/pkg-plist
1.8 audio/xmms-arts_output/Makefile
1.4 audio/xmms-arts_output/distinfo
1.2 audio/xmms-arts_output/files/patch-arts_helper.c

(Only the first 10 of 366 ports in this commit are shown above. View all ports for this commit)
As previously announced, remove ports that have reached their expiry date,
and the handful of ports that depended on them.
Fri, 26 Nov 2004
[ 16:34 sem ] Original commit 
1.66 biology/Makefile
1.1 biology/embassy/Makefile
1.1 biology/embassy/distinfo
1.1 biology/embassy/pkg-descr
1.1 biology/embassy/pkg-plist
[new port] biology/embassy

PR:             ports/74330
Submitted by:   Fernan Aguero <fernan(at)iib.unsam.edu.ar>
Thu, 11 Nov 2004
[ 21:35 pav ] Original commit 
1.367 LEGAL
1.65 biology/Makefile
1.1 biology/blast/Makefile
1.1 biology/blast/distinfo
1.1 biology/blast/files/pkg-message.in
1.1 biology/blast/pkg-descr
1.1 biology/blast/pkg-plist
Add blast, a powerful software package for gene and protein identification,
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>
Tue, 22 Jun 2004
[ 14:29 krion ] Original commit 
1.64 biology/Makefile
1.1 biology/ariadne/Makefile
1.1 biology/ariadne/distinfo
1.1 biology/ariadne/pkg-descr
1.1 biology/ariadne/pkg-plist
Add ariadne 1.3, programs to compare protein sequences and
profiles, using the Smith-Waterman algorithm.

PR:             ports/67811
Submitted by:   Fernan Aguero <fernan@iib.unsam.edu.ar>
Fri, 2 Apr 2004
[ 07:29 kris ] Original commit 
1.5 accessibility/Makefile
1.2 accessibility/pkg/COMMENT
1.5 arabic/Makefile
1.2 arabic/pkg/COMMENT
1.96 archivers/Makefile
1.3 archivers/pkg/COMMENT
1.78 astro/Makefile
1.3 astro/pkg/COMMENT
1.505 audio/Makefile
1.3 audio/pkg/COMMENT

(Only the first 10 of 120 ports in this commit are shown above. View all ports for this commit)
Remove category pkg/COMMENT files in favour of a COMMENT variable in the
category makefile.

Submitted by:   Matthew Seaman <m.seaman@infracaninophile.co.uk>
PR:             59651
Wed, 3 Sep 2003
[ 02:23 edwin ] Original commit 
1.62 biology/Makefile
1.1 biology/lsysexp/Makefile
1.1 biology/lsysexp/distinfo
1.1 biology/lsysexp/pkg-descr
1.1 biology/lsysexp/pkg-plist
new port:biology/lsysexp

        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>
Fri, 8 Aug 2003
[ 03:31 kris ] Original commit 
1.61 biology/Makefile
As announced on May 6, remove the broken p5-bioperl-devel port.
Mon, 28 Jul 2003
[ 06:38 maho ] Original commit 
1.60 biology/Makefile
1.1 biology/garlic/Makefile
1.1 biology/garlic/distinfo
1.1 biology/garlic/files/patch-Makefile
1.1 biology/garlic/pkg-descr
1.1 biology/garlic/pkg-plist
A new port garlic, free molecular viewer and editor, free molecular
visualization program, protein structure, DNA structure, PDB,
molecular rendering, biological macromolecule.
Wed, 5 Feb 2003
[ 09:01 kris ] Original commit 
1.59 biology/Makefile
Remove gaussian98

Pointy hat to:  maho
Thu, 16 Jan 2003
[ 14:22 edwin ] Original commit 
1.58 biology/Makefile
1.1 biology/act/Makefile
1.1 biology/act/distinfo
1.1 biology/act/pkg-comment
1.1 biology/act/pkg-descr
1.1 biology/act/pkg-plist
New Port: biology/act

PR:             ports/35753
Submitted by:   Camson Huynh <chuynh@biolateral.com.au>
Wed, 20 Nov 2002
[ 08:54 ijliao ] Original commit 
1.57 biology/Makefile
1.1 biology/treepuzzle/Makefile
1.1 biology/treepuzzle/distinfo
1.1 biology/treepuzzle/pkg-comment
1.1 biology/treepuzzle/pkg-descr
1.1 biology/treepuzzle/pkg-plist
add treepuzzle 5.1
Maximum likelihood phylogeny reconstruction using quartets

PR:             45241
Submitted by:   Jan Lentfer <lentferj@neslonek.bio.tu-darmstadt.de>
Mon, 7 Oct 2002
[ 03:08 lioux ] Original commit 
1.56 biology/Makefile
Connect distribfold to build after moving it from misc category

Prompted by:    kris,
                Adam Weinberger <adam@vectors.cx>,
                Fernan Aguero <fernan@iib.unsam.edu.ar>,
                others
Tue, 17 Sep 2002
[ 15:31 ijliao ] Original commit 
1.55 biology/Makefile
1.1 biology/primer3/Makefile
1.1 biology/primer3/distinfo
1.1 biology/primer3/pkg-comment
1.1 biology/primer3/pkg-descr
1.1 biology/primer3/pkg-plist
add primer3 0.9
Primer3 helps to choose primers for PCR reactions

PR:             35298
Submitted by:   Tony Maher <tonym@biolateral.com.au>

Number of commits found: 109 (showing only 100 on this page)

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