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sci-biology/aaindex

Amino acid indices and similarity matrices

09 Aug 2011; Kacper Kowalik (xarthisius) aaindex-9.1.ebuild:
ppc64 keyword dropped
alphaamd64armhppaia64ppcppc64sparcx86
9.1 + + +
sci-biology Homepage public-domain ChangeLog Metadata Similar Bugs Forums

sci-biology/abyss

Assembly By Short Sequences - a de novo, parallel, paired-end sequence assembler

*abyss-1.3.4 (20 Jun 2012)
20 Jun 2012; Justin Lecher (jlec) abyss-1.3.0.ebuild,
abyss-1.3.3.ebuild, +files/abyss-1.3.3-gcc-4.7.patch, +abyss-1.3.4.ebuild,
+files/abyss-1.3.4-gcc-4.7.patch:
Fix compilation with gcc-4.7, #422599; install docs inside /usr/share/doc/,
#297205
alphaamd64armhppaia64ppcppc64sparcx86
1.3.4 ~ ~
1.3.3 ~ ~
1.3.0 ~ ~
1.2.7 + +
1.2.3 + +
sci-biology Homepage abyss ChangeLog Metadata Similar Bugs Forums

sci-biology/allpaths

De novo assembly of whole-genome shotgun microreads

19 Nov 2012; Justin Lecher (jlec) allpaths-2.0.ebuild,
allpaths-3.1.ebuild, allpaths-3.1-r1.ebuild:
Block sci-biology/allpathslg due to file collision, #443740
alphaamd64armhppaia64ppcppc64sparcx86
3.1-r1 ~ ~
3.1 ~ ~
2.0 + +
sci-biology Homepage Whitehead-MIT ChangeLog Metadata Similar Bugs Forums

sci-biology/allpathslg

De novo assembly of whole-genome shotgun microreads

20 Feb 2013; Agostino Sarubbo (ago) allpathslg-42337.ebuild:
Stable for amd64, wrt bug #458106
alphaamd64armhppaia64ppcppc64sparcx86
42337 +
sci-biology Homepage MIT ChangeLog Metadata Similar Bugs Forums

sci-biology/amap

Protein multiple-alignment-based sequence annealing

*amap-2.2-r2 (26 Mar 2011)
26 Mar 2011; Kacper Kowalik (xarthisius) -amap-2.2-r1.ebuild,
+amap-2.2-r2.ebuild, -files/amap-2.2-cxxflags.patch,
-files/amap-2.2-gcc4.3.patch, +files/amap-2.2-includes.patch,
+files/amap-2.2-makefile.patch:
Clean java bits thanks to sera. General cleanup, fix linking order, fix
building with gcc 4.6 wrt #360517. Drop old.
alphaamd64armhppaia64ppcppc64sparcx86
2.2-r2 ~ ~
sci-biology Homepage GPL-2 ChangeLog Metadata Similar Bugs Forums

sci-biology/amos

A Modular, Open-Source whole genome assembler

19 Mar 2013; Justin Lecher (jlec) amos-3.1.0.ebuild, metadata.xml:
Change USE name from qt to qt4, #462218
alphaamd64armhppaia64ppcppc64sparcx86
3.1.0 + +
sci-biology Homepage Artistic ChangeLog Metadata Similar Bugs Forums

sci-biology/ApE

ApE - A Plasmid Editor

*ApE-2.0.7-r1 (31 Dec 2012)
31 Dec 2012; Jeff Gardner (je_fro) +ApE-2.0.7-r1.ebuild:
Forward command line arguments to ApE startup script, thanks to Markus Meier
in bug #375919
alphaamd64armhppaia64ppcppc64sparcx86
2.0.7-r1 ~ ~
2.0.7 ~ ~
sci-biology Homepage ApE ChangeLog Metadata Similar Bugs Forums

sci-biology/arb

Tools for DNA/RNA sequence database handling and data analysis, phylogenetic analysis

24 Oct 2012; Ulrich Müller (ulm) arb-5.1-r1.ebuild,
arb-5.2.ebuild, arb-5.3.ebuild:
Update dependency after package move from x11-libs/openmotif to
x11-libs/motif.
alphaamd64armhppaia64ppcppc64sparcx86
5.3 ~ ~
5.2 ~ ~
5.1-r1 ~ ~
sci-biology Homepage arb ChangeLog Metadata Similar Bugs Forums

sci-biology/ariadne

Protein sequences and profiles comparison

11 Apr 2013; Ulrich Müller (ulm) ariadne-1.3-r1.ebuild,
ariadne-1.3-r2.ebuild:
Fix LICENSE, see README and notices in source files.
alphaamd64armhppaia64ppcppc64sparcx86
1.3-r2 ~ ~
1.3-r1 ~ +
sci-biology Homepage ARIADNE ChangeLog Metadata Similar Bugs Forums

sci-biology/augustus

Eukaryotic gene predictor

31 Jan 2013; Agostino Sarubbo (ago) augustus-2.5.5.ebuild:
Stable for x86, wrt bug #454842
alphaamd64armhppaia64ppcppc64sparcx86
2.5.5 + +
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sci-biology/bamtools

A programmer's API and an end-user's toolkit for handling BAM files

01 Mar 2013; Justin Lecher (jlec) bamtools-2.2.3.ebuild,
files/bamtools-2.2.3-unbundle.patch:
Update script and correct dep on jsoncpp
alphaamd64armhppaia64ppcppc64sparcx86
2.2.3 ~ ~
1.0.2 ~ ~
sci-biology Homepage MIT ChangeLog Metadata Similar Bugs Forums

sci-biology/beast-mcmc

Bayesian MCMC of Evolution & Phylogenetics using Molecular Sequences

*beast-mcmc-1.7.5 (18 Feb 2013)
18 Feb 2013; Justin Lecher (jlec) +beast-mcmc-1.7.5.ebuild,
metadata.xml:
Version Bump, fixes missing package, #374277
alphaamd64armhppaia64ppcppc64sparcx86
9999
1.7.5
1.5.2 ~ ~
sci-biology Homepage LGPL-3 ChangeLog Metadata Similar Bugs Forums

sci-biology/bedtools

Tools for manipulation and analysis of BED, GFF/GTF, VCF, and SAM/BAM file formats

*bedtools-2.16.2 (29 May 2012)
29 May 2012; Andrey Kislyuk (weaver) +bedtools-2.16.2.ebuild,
-bedtools-2.13.3.ebuild, -bedtools-2.15.0.ebuild:
version bump
alphaamd64armhppaia64ppcppc64sparcx86
2.16.2 ~ ~
sci-biology Homepage GPL-2 ChangeLog Metadata Similar Bugs Forums

sci-biology/bfast

17 Feb 2013; Justin Lecher (jlec) bfast-0.7.0a.ebuild:
Build in source for tests
alphaamd64armhppaia64ppcppc64sparcx86
0.7.0a
sci-biology Homepages: ChangeLog Metadata Similar Bugs Forums

sci-biology/biogrep

Multithreading application for matching large sets of patternsagainst biosequence dbs

*biogrep-1.0-r1 (10 Oct 2010)
10 Oct 2010; Justin Lecher (jlec) +biogrep-1.0-r1.ebuild,
metadata.xml:
Package taken, respect CC now
alphaamd64armhppaia64ppcppc64sparcx86
1.0-r1 ~ ~
1.0 ~ ~
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sci-biology/bioperl

Perl tools for bioinformatics - Core modules

24 Mar 2012; Raúl Porcel (armin76) bioperl-1.5.1-r1.ebuild:
Drop alpha/ia64/sparc keywords
alphaamd64armhppaia64ppcppc64sparcx86
9999-r1
1.6.9 ~ ~
1.6.0-r2 + +
sci-biology Homepage Artistic GPL-2 ChangeLog Metadata Similar Bugs Forums

sci-biology/bioperl-db

Perl tools for bioinformatics - Perl API that accesses the BioSQL schema

23 Jun 2012; Justin Lecher (jlec) bioperl-db-1.6.9.ebuild:
Add missing DEP on dev-perl/DBD-mysql, #422999
alphaamd64armhppaia64ppcppc64sparcx86
9999-r1
1.6.9 ~ ~
1.6.0 + +
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sci-biology/bioperl-network

Perl tools for bioinformatics - Analysis of protein-protein interaction networks

20 Sep 2011; Michał Górny (mgorny)
bioperl-network-9999-r1.ebuild:
Migrate to git-2.
alphaamd64armhppaia64ppcppc64sparcx86
9999-r1
1.6.9 ~ ~
1.6.0 + +
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sci-biology/bioperl-run

Perl tools for bioinformatics - Wrapper modules around key bioinformatics applications

20 Sep 2011; Michał Górny (mgorny) bioperl-run-9999-r1.ebuild:
Migrate to git-2.
alphaamd64armhppaia64ppcppc64sparcx86
9999-r1
1.6.9 ~ ~
1.6.1 + +
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sci-biology/biopython

Python modules for computational molecular biology

*biopython-1.61 (26 Apr 2013)
26 Apr 2013; Justin Lecher (jlec) +biopython-1.61.ebuild,
metadata.xml:
Version Bump
alphaamd64armhppaia64ppcppc64sparcx86
1.61 ~ ~ ~
1.59 ~ ~ ~
1.58 ~ ~ ~
1.57 + + +
sci-biology Homepages: 1 2 HPND ChangeLog Metadata Similar Bugs Forums

sci-biology/bioruby

An integrated environment for bioinformatics using the Ruby language

*bioruby-1.4.2 (28 Nov 2011)
28 Nov 2011; Andrey Kislyuk (weaver) +bioruby-1.4.2.ebuild:
Version bump
alphaamd64armhppaia64ppcppc64sparcx86
9999
1.4.2 ~ ~ ~
1.3.1 + ~ +
1.3.0 ~ ~ ~
1.1.0 ~ ~
sci-biology Homepage Ruby ChangeLog Metadata Similar Bugs Forums

sci-biology/biosql

A generic bioinformatics relational database model

02 Jun 2009; Christian Faulhammer (fauli) biosql-1.0.1.ebuild:
stable x86, bug 270587
alphaamd64armhppaia64ppcppc64sparcx86
1.0.1 + +
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sci-biology/blat

The BLAST-Like Alignment Tool, a fast genomic sequence aligner

04 Aug 2011; Fabian Groffen (grobian) blat-34-r1.ebuild:
Marked ~x64-macos, bug #375521
alphaamd64armhppaia64ppcppc64sparcx86
34-r1 ~ ~
34 + +
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sci-biology/blossoc

A linkage disequilibrium association mapping tool

20 Jun 2010; Kacper Kowalik (xarthisius) blossoc-1.4.0.ebuild,
+files/blossoc-1.4.0-gcc43.patch:
Fixing build with gcc-4.3. Thanks Sebastian Luther
<SebastianLuther@gmx.de> for report and patch
alphaamd64armhppaia64ppcppc64sparcx86
1.4.0 + +
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sci-biology/bowtie

An ultrafast memory-efficient short read aligner

*bowtie-0.12.8 (19 Jun 2012)
19 Jun 2012; Justin Lecher (jlec) +bowtie-0.12.8.ebuild,
+files/bowtie-0.12.8-gcc-47.patch:
Version Bump, Fix compilation with gcc-4.7, #421919
alphaamd64armhppaia64ppcppc64sparcx86
0.12.8 ~ ~
0.12.7 ~ ~
0.12.5 ~ ~
0.12.3 + +
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sci-biology/bwa

Burrows-Wheeler Alignment Tool, a fast short genomic sequence aligner

*bwa-0.6.2 (21 Jan 2013)
21 Jan 2013; Andrey Kislyuk (weaver) +bwa-0.6.2.ebuild:
Version bump
alphaamd64armhppaia64ppcppc64sparcx86
0.6.2 ~ ~
0.6.1 ~ ~
0.5.9 ~ ~
0.5.0-r1 ~ ~
0.5.0 + +
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sci-biology/cd-hit

Clustering Database at High Identity with Tolerance

*cd-hit-4.6 (20 Jun 2012)
20 Jun 2012; Justin Lecher (jlec) +files/4.6-gentoo.patch,
cd-hit-4.5.1.ebuild, cd-hit-4.5.4.ebuild, +cd-hit-4.6.ebuild, metadata.xml:
Version Bump, which fixes compilation problems with gcc 4.7, #422569; add
missing eutils.eclass
alphaamd64armhppaia64ppcppc64sparcx86
4.6 ~ ~
4.5.4 ~ ~
4.5.1 ~ ~
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sci-biology/clustal-omega

Scalable multiple alignment of protein sequences

*clustal-omega-1.1.0 (26 Apr 2013)
26 Apr 2013; Justin Lecher (jlec) +clustal-omega-1.1.0.ebuild:
Version BUmp
alphaamd64armhppaia64ppcppc64sparcx86
1.1.0 ~ ~
1.0.3 ~ ~
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sci-biology/clustalw

General purpose multiple alignment program for DNA and proteins

13 Jun 2012; Johannes Huber (johu) clustalw-2.1.ebuild:
Stable for x86, wrt bug #416891
alphaamd64armhppaia64ppcppc64sparcx86
2.1 + +
2.0.12 ~ ~
2.0.11 + +
1.83-r3 ~ ~ ~ ~ ~ ~
1.83-r2 + + + + + +
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sci-biology/clustalw-mpi

A parallel (MPI) implemention of the Clustal-W general purpose multiple alignment algorithm

*clustalw-mpi-0.13-r1 (19 Jun 2011)
19 Jun 2011; Justin Lecher (jlec) +files/0.13-gentoo.patch,
-clustalw-mpi-0.13.ebuild, +clustalw-mpi-0.13-r1.ebuild:
Respect LDFLAGS, #335232
alphaamd64armhppaia64ppcppc64sparcx86
0.13-r1 ~ ~
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sci-biology/clustalx

Graphical interface for the ClustalW multiple alignment program

02 Mar 2013; Markos Chandras (hwoarang) clustalx-2.1.ebuild:
Move Qt dependencies to the new category
alphaamd64armhppaia64ppcppc64sparcx86
2.1 + +
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sci-biology/consed

A genome sequence finishing program

17 Feb 2013; Justin Lecher (jlec) consed-19-r2.ebuild,
metadata.xml:
Quote EPREFIX, thanks Martin Mokrejš for the patch
alphaamd64armhppaia64ppcppc64sparcx86
19-r2 ~ ~
19-r1 ~ ~
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sci-biology/cufflinks

Transcript assembly, differential expression, and differential regulation for RNA-Seq

10 Nov 2012; Justin Lecher (jlec) cufflinks-1.3.0.ebuild,
+files/cufflinks-1.3.0-autotools.patch, +files/cufflinks-1.3.0-boost.patch,
+files/cufflinks-1.3.0-gcc-4.7.patch:
Drop hard version dep for boost, #440630, and fix compatibility with version
1.5*; Fix gcc-4.7 problems; Fix underlinking problem
alphaamd64armhppaia64ppcppc64sparcx86
1.3.0 M~ M~
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sci-biology/cutg

Codon usage tables calculated from GenBank

09 Aug 2011; Kacper Kowalik (xarthisius) cutg-151.ebuild,
cutg-160.ebuild:
ppc64 keyword dropped
alphaamd64armhppaia64ppcppc64sparcx86
160 + ~ +
151 + + +
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sci-biology/dialign-tx

Greedy and progressive approaches for segment-based multiple sequence alignment

*dialign-tx-1.0.2-r1 (09 Sep 2010)
09 Sep 2010; Kacper Kowalik (xarthisius)
+dialign-tx-1.0.2-r1.ebuild, +files/dialign-tx-1.0.2-implicits.patch:
Respect LDFLAGS wrt bug 336533. Thanks to Diego for the report. Fix
implicit function declarations.
alphaamd64armhppaia64ppcppc64sparcx86
1.0.2-r1 ~ ~
1.0.2 + +
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sci-biology/diya

Do It Yourself Annotation, a collection of tools and libraries for sequence assembly and annotation

*diya-1.0_rc4 (27 Sep 2009)
27 Sep 2009; Andrey Kislyuk (weaver) +metadata.xml,
+diya-1.0_rc4.ebuild:
New package, ebuild written by me
alphaamd64armhppaia64ppcppc64sparcx86
1.0_rc4 ~ ~
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sci-biology/elph

Estimated Locations of Pattern Hits - Motif finder program

09 Aug 2010; Kacper Kowalik (xarthisius) elph-1.0.1.ebuild:
Respect LDFLAGS wrt bug 331881. Thanks to Diego for report.
alphaamd64armhppaia64ppcppc64sparcx86
1.0.1 ~ ~
0.1.5 +
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sci-biology/embassy

A meta-package for installing all EMBASSY packages (EMBOSS add-ons)

09 Mar 2011; Raúl Porcel (armin76) embassy-4.0.0.ebuild,
embassy-6.0.1.ebuild, embassy-6.1.0.ebuild:
Drop sparc keywords
alphaamd64armhppaia64ppcppc64sparcx86
6.1.0 ~ ~ ~
6.0.1 + ~ +
sci-biology Homepage GPL-2 freedist ChangeLog Metadata Similar Bugs Forums

sci-biology/embassy-cbstools

EMBOSS wrappers for applications from the CBS group

20 Oct 2011; Kacper Kowalik (xarthisius)
embassy-cbstools-1.0.0.ebuild, embassy-cbstools-1.0.0-r1.ebuild:
Fix SRC_URI for emboss
alphaamd64armhppaia64ppcppc64sparcx86
1.0.0-r1 ~ ~ ~
1.0.0 + ~ +
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sci-biology/embassy-domainatrix

Protein domain analysis add-on package for EMBOSS

20 Oct 2011; Kacper Kowalik (xarthisius)
embassy-domainatrix-0.1.0-r3.ebuild, embassy-domainatrix-0.1.0-r4.ebuild:
Fix SRC_URI for emboss
alphaamd64armhppaia64ppcppc64sparcx86
0.1.0-r4 ~ ~ ~
0.1.0-r3 + ~ +
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sci-biology/embassy-domalign

Protein domain alignment add-on package for EMBOSS

20 Oct 2011; Kacper Kowalik (xarthisius)
embassy-domalign-0.1.0-r4.ebuild, embassy-domalign-0.1.0-r3.ebuild:
Fix SRC_URI for emboss
alphaamd64armhppaia64ppcppc64sparcx86
0.1.0-r4 ~ ~ ~
0.1.0-r3 + ~ +
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sci-biology/embassy-domsearch

Protein domain search add-on package for EMBOSS

20 Oct 2011; Kacper Kowalik (xarthisius)
embassy-domsearch-0.1.0-r4.ebuild, embassy-domsearch-0.1.0-r3.ebuild:
Fix SRC_URI for emboss
alphaamd64armhppaia64ppcppc64sparcx86
0.1.0-r4 ~ ~ ~
0.1.0-r3 + ~ +
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sci-biology/embassy-emnu

EMBOSS Menu is Not UNIX - Simple menu of EMBOSS applications

20 Oct 2011; Kacper Kowalik (xarthisius)
embassy-emnu-1.05-r5.ebuild, embassy-emnu-1.05-r6.ebuild:
Fix SRC_URI for emboss
alphaamd64armhppaia64ppcppc64sparcx86
1.05-r6 ~ ~ ~
1.05-r5 + ~ +
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sci-biology/embassy-esim4

EMBOSS integrated version of sim4 - Alignment of cDNA and genomic DNA

20 Oct 2011; Kacper Kowalik (xarthisius)
embassy-esim4-1.0.0-r6.ebuild, embassy-esim4-1.0.0-r5.ebuild:
Fix SRC_URI for emboss
alphaamd64armhppaia64ppcppc64sparcx86
1.0.0-r6 ~ ~ ~
1.0.0-r5 + ~ +
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sci-biology/embassy-hmmer

EMBOSS wrappers for HMMER - Biological sequence analysis with profile HMMs

20 Oct 2011; Kacper Kowalik (xarthisius)
embassy-hmmer-2.3.2-r3.ebuild, embassy-hmmer-2.3.2-r2.ebuild:
Fix SRC_URI for emboss
alphaamd64armhppaia64ppcppc64sparcx86
2.3.2-r3 ~ ~ ~
2.3.2-r2 + ~ +
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sci-biology/embassy-iprscan

InterProScan motif detection add-on package for EMBOSS

20 Oct 2011; Kacper Kowalik (xarthisius)
embassy-iprscan-4.3.1-r1.ebuild, embassy-iprscan-4.3.1.ebuild:
Fix SRC_URI for emboss
alphaamd64armhppaia64ppcppc64sparcx86
4.3.1-r1 ~ ~ ~
4.3.1 + ~ +
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sci-biology/embassy-memenew

EMBOSS wrappers for MEME - Multiple Em for Motif Elicitation

20 Oct 2011; Kacper Kowalik (xarthisius)
embassy-memenew-0.1.0-r1.ebuild, embassy-memenew-4.0.0.ebuild:
Fix SRC_URI for emboss
alphaamd64armhppaia64ppcppc64sparcx86
4.0.0 ~ ~ ~
0.1.0-r1 + ~ +
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sci-biology/embassy-mira

Fragment assembly add-on package for EMBOSS

20 Oct 2011; Kacper Kowalik (xarthisius)
embassy-mira-2.8.2.ebuild, embassy-mira-2.8.2-r1.ebuild:
Fix SRC_URI for emboss wrt #387299
alphaamd64armhppaia64ppcppc64sparcx86
2.8.2-r1 ~ ~ ~
2.8.2 + ~ +
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sci-biology/embassy-mse

EMBOSS integrated version of MSE - Multiple Sequence Screen Editor

20 Oct 2011; Kacper Kowalik (xarthisius)
embassy-mse-1.0.0-r6.ebuild, embassy-mse-1.0.0-r7.ebuild:
Fix SRC_URI for emboss
alphaamd64armhppaia64ppcppc64sparcx86
1.0.0-r7 ~ ~ ~
1.0.0-r6 + ~ +
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sci-biology/embassy-phylipnew

EMBOSS integrated version of PHYLIP - The Phylogeny Inference Package

20 Oct 2011; Kacper Kowalik (xarthisius)
embassy-phylipnew-3.68.ebuild, embassy-phylipnew-3.67.ebuild:
Fix SRC_URI for emboss
alphaamd64armhppaia64ppcppc64sparcx86
3.68 ~ ~ ~
3.67 + ~ +
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sci-biology/embassy-signature

Protein signature add-on package for EMBOSS

20 Oct 2011; Kacper Kowalik (xarthisius)
embassy-signature-0.1.0-r3.ebuild, embassy-signature-0.1.0-r4.ebuild:
Fix SRC_URI for emboss
alphaamd64armhppaia64ppcppc64sparcx86
0.1.0-r4 ~ ~ ~
0.1.0-r3 + ~ +
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sci-biology/embassy-structure

Protein structure add-on package for EMBOSS

20 Oct 2011; Kacper Kowalik (xarthisius)
embassy-structure-0.1.0-r4.ebuild, embassy-structure-0.1.0-r3.ebuild:
Fix SRC_URI for emboss
alphaamd64armhppaia64ppcppc64sparcx86
0.1.0-r4 ~ ~ ~
0.1.0-r3 + ~ +
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sci-biology/embassy-topo

EMBOSS integrated version of TOPO - Transmembrane protein display

20 Oct 2011; Kacper Kowalik (xarthisius)
embassy-topo-1.0.0-r5.ebuild, embassy-topo-1.0.0-r6.ebuild:
Fix SRC_URI for emboss
alphaamd64armhppaia64ppcppc64sparcx86
1.0.0-r6 ~ ~ ~
1.0.0-r5 + ~ +
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sci-biology/embassy-vienna

EMBOSS integrated version of the Vienna RNA package - RNA folding

20 Oct 2011; Kacper Kowalik (xarthisius)
embassy-vienna-1.7.2.ebuild, embassy-vienna-1.7.2-r1.ebuild:
Fix SRC_URI for emboss
alphaamd64armhppaia64ppcppc64sparcx86
1.7.2-r1 ~ ~ ~
1.7.2 + ~ +
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sci-biology/emboss

The European Molecular Biology Open Software Suite - A sequence analysis package

*emboss-6.3.1_p4-r1 (19 Nov 2012)
19 Nov 2012; Justin Lecher (jlec) +emboss-6.3.1_p4-r1.ebuild,
+files/emboss-6.3.1_p4-r1_plcol.patch:
Fix compilation problem with toplplot, #391669, thanks Juergen Rose for the
patch
alphaamd64armhppaia64ppcppc64sparcx86
6.3.1_p4-r1 ~ ~ ~
6.3.1_p4 ~ ~ ~
6.1.0-r1 ~ ~ ~
6.0.1 + + +
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sci-biology/eugene

*eugene-4.1 (09 Mar 2013)
09 Mar 2013; Justin Lecher (jlec) +eugene-4.1.ebuild,
metadata.xml:
Version Bump; drop maintainer
alphaamd64armhppaia64ppcppc64sparcx86
4.1
3.6-r1 + +
3.5g + +
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sci-biology/exonerate

Generic tool for pairwise sequence comparison

25 Jan 2013; Justin Lecher (jlec) exonerate-2.2.0-r1.ebuild,
metadata.xml:
We need USE=utils for testing, #453978; move to autotool-utils.eclass
alphaamd64armhppaia64ppcppc64sparcx86
2.2.0-r1 ~ ~
2.2.0 ~ ~
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sci-biology/express

Streaming RNA-Seq Analysis

09 Nov 2012; Justin Lecher (jlec) express-0.9.5.ebuild:
Keyworded for ~x86; drop needless version restriction of boost, #440634
alphaamd64armhppaia64ppcppc64sparcx86
0.9.5 M~ M~
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sci-biology/fasta

FASTA is a DNA and Protein sequence alignment software package

*fasta-36.3.5e (11 May 2013)
11 May 2013; Justin Lecher (jlec) +fasta-36.3.5e.ebuild,
+files/fasta-36.3.5e-ldflags.patch:
Version BUmp
alphaamd64armhppaia64ppcppc64sparcx86
36.3.5e ~ ~ ~
35.4.10 + ~ +
sci-biology Homepage fasta ChangeLog Metadata Similar Bugs Forums

sci-biology/fasttree

Fast inference of approximately-maximum-likelihood phylogenetic trees

20 Jun 2010; Kacper Kowalik (xarthisius) fasttree-2.0.1.ebuild,
+files/fasttree-2.0.1-asneeded.patch:
Respect FLAGS and fix as-needed issues wrt bug 295199. Thanks Diego for
reporting.
alphaamd64armhppaia64ppcppc64sparcx86
2.0.1 ~ ~
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sci-biology/finchtv

Graphical viewer for chromatogram files

24 Jul 2012; Justin Lecher (jlec) finchtv-1.3.1-r1.ebuild,
metadata.xml:
Use QA_PREBUILT for binary packages
alphaamd64armhppaia64ppcppc64sparcx86
1.3.1-r1 + +
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sci-biology/foldingathome

Folding@Home is a distributed computing project for protein folding.

13 May 2013; Ian Stakenvicius (axs) foldingathome-7.3.6-r2.ebuild:
showing special permission during pkg_setup so that we 'display this notice.'
alphaamd64armhppaia64ppcppc64sparcx86
7.3.6-r2 ~ ~
sci-biology Homepage FAH-EULA-2009 FAH-special-permission ChangeLog Metadata Similar Bugs Forums

sci-biology/gatk

*gatk-2.4 (11 Mar 2013)
11 Mar 2013; Justin Lecher (jlec) -gatk-1.6.ebuild,
+gatk-2.4.ebuild, gatk-9999.ebuild:
Version BUmp and move to MIT license
alphaamd64armhppaia64ppcppc64sparcx86
9999
2.4
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sci-biology/GBrowse

Generic Model Organism Database Project - The Generic Genome Browser

*GBrowse-2.48 (27 Feb 2012)
27 Feb 2012; Andrey Kislyuk (weaver) -GBrowse-2.39.ebuild,
+GBrowse-2.48.ebuild:
Version bump
alphaamd64armhppaia64ppcppc64sparcx86
2.48 ~ ~
2.44-r1 ~ ~
sci-biology Homepage || ( Artistic GPL-1 GPL-2 GPL-3 ) ChangeLog Metadata Similar Bugs Forums

sci-biology/gibbs

Identify motifs, conserved regions, in DNA or protein sequences

26 Apr 2012; Justin Lecher (jlec) gibbs-3.1.ebuild,
-gibbs-1995.9.ebuild:
Move to EAPI=4, drop old
alphaamd64armhppaia64ppcppc64sparcx86
3.1 + +
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sci-biology/glimmer

An HMM-based microbial gene finding system from TIGR

16 Jul 2010; Markos Chandras (hwoarang) glimmer-3.02-r2.ebuild:
Stable on amd64 wrt bug #328415
alphaamd64armhppaia64ppcppc64sparcx86
3.02-r2 + +
3.02-r1 + +
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sci-biology/glimmerhmm

An eukaryotic gene finding system from TIGR

18 Oct 2012; Justin Lecher (jlec) -glimmerhmm-3.0.1.ebuild:
Drop old
alphaamd64armhppaia64ppcppc64sparcx86
3.0.1-r1 + +
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sci-biology/gmap

A Genomic Mapping and Alignment Program for mRNA and EST Sequences

*gmap-2012.07.20 (05 Oct 2012)
05 Oct 2012; Andrey Kislyuk (weaver) -gmap-2010.07.27.ebuild,
-gmap-2011.03.28.ebuild, -gmap-2011.09.14.ebuild, +gmap-2012.07.20.ebuild:
Version bump, remove old
alphaamd64armhppaia64ppcppc64sparcx86
2012.07.20 ~ ~
2011.10.07 ~ ~
sci-biology Homepage gmap ChangeLog Metadata Similar Bugs Forums

sci-biology/goby

A DNA sequencing data management framework

*goby-1.9.8.1 (05 Jan 2012)
05 Jan 2012; Andrey Kislyuk (weaver) +goby-1.9.8.1.ebuild:
Version bump
alphaamd64armhppaia64ppcppc64sparcx86
1.9.8.1 ~ ~
1.9.7.3 ~ ~
sci-biology Homepage GPL-3 LGPL-3 ChangeLog Metadata Similar Bugs Forums

sci-biology/goby-cpp

A DNA sequencing data management framework - C/C++ API

*goby-cpp-2.0.1 (19 Jul 2012)
19 Jul 2012; Justin Lecher (jlec) +goby-cpp-2.0.1.ebuild:
Version Bump, handle static-libs
alphaamd64armhppaia64ppcppc64sparcx86
2.0.1 ~ ~
1.9.8.1 ~ ~
1.9.7.3 ~ ~
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sci-biology/hmmer

Sequence analysis using profile hidden Markov models

28 Jun 2012; Justin Lecher (jlec) hmmer-3.0.ebuild,
-files/hmmer-3.0-perl-5.16.patch:
Fix the patch, thanks xarthisius and bonsaikitten for help
alphaamd64armhppaia64ppcppc64sparcx86
3.0 + +
2.3.2-r2 ~ + ~ ~ + ~ +
2.3.2-r1 ~ + + ~ ~ +
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sci-biology/iedera

A subset seed design tool for DNA sequence alignment

*iedera-1.04 (18 Jun 2010)
18 Jun 2010; Andrey Kislyuk (weaver) +metadata.xml,
+iedera-1.04.ebuild:
New package, ebuild written by me
alphaamd64armhppaia64ppcppc64sparcx86
1.04 ~ ~
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sci-biology/infernal

Inference of RNA alignments

25 Jun 2012; Justin Lecher (jlec) infernal-1.0.2-r1.ebuild,
+files/infernal-1.0.2-perl-5.16.patch:
Fix for perl-5.16, #422561; move to EAPI=4
alphaamd64armhppaia64ppcppc64sparcx86
1.0.2-r1 + +
sci-biology Homepage GPL-3 ChangeLog Metadata Similar Bugs Forums

sci-biology/iqpnni

Important Quartet Puzzling and NNI Operation

*iqpnni-3.3.2 (25 Sep 2011)
25 Sep 2011; Andrey Kislyuk (weaver) +iqpnni-3.3.2.ebuild:
Version bump
alphaamd64armhppaia64ppcppc64sparcx86
3.3.2 ~ ~
3.3.1 + +
3.2 ~ ~
sci-biology Homepage GPL-2 ChangeLog Metadata Similar Bugs Forums

sci-biology/kalign

Global and progressive multiple sequence alignment

18 Dec 2011; Pawel Hajdan jr (phajdan.jr) kalign-2.03-r1.ebuild:
x86 stable wrt bug #393791
alphaamd64armhppaia64ppcppc64sparcx86
2.03-r1 + +
2.03 + +
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sci-biology/lagan

LAGAN, Multi-LAGAN, Shuffle-LAGAN, Supermap: Whole-genome multiple alignment of genomic DNA

*lagan-2.0-r2 (12 Sep 2010)
12 Sep 2010; Justin Lecher (jlec) +lagan-2.0-r2.ebuild,
+files/lagan-2.0-flags.patch:
Fix respect of FLAGS, 334951; do not install ELF in /usr/share, 296021
alphaamd64armhppaia64ppcppc64sparcx86
2.0-r2 ~ ~
2.0-r1 ~ ~
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sci-biology/last

Genome-scale comparison of biological sequences

*last-230 (20 Jun 2012)
20 Jun 2012; Justin Lecher (jlec) +last-230.ebuild:
Version BUmp, allows to compile with gcc-4.7, #422573
alphaamd64armhppaia64ppcppc64sparcx86
230 ~ ~
192 ~ ~
184 ~ ~
162-r1 + +
146 + +
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sci-biology/mafft

Multiple sequence alignments using a variety of algorithms

*mafft-7.043 (26 May 2013)
26 May 2013; Justin Lecher (jlec) mafft-7.040.ebuild,
+mafft-7.043.ebuild:
Version Bump, add test function
alphaamd64armhppaia64ppcppc64sparcx86
7.043 ~ ~
7.040 ~ ~
7.037 ~ ~
6.811 ~ ~
6.707 ~ ~
6.240-r1 ~ ~
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sci-biology/mammoth

MAtching Molecular Models Obtained from THeory

19 Oct 2012; Justin Lecher (jlec) mammoth-1.0.ebuild,
metadata.xml:
Remove virtual/fortran and always call fortran-2_pkg_setup as intend by the
updated fortran-2.eclass
alphaamd64armhppaia64ppcppc64sparcx86
1.0 ~ ~
sci-biology Homepage mammoth ChangeLog Metadata Similar Bugs Forums

sci-biology/maq

Mapping and Assembly with Qualities - mapping Solexa and SOLiD reads to reference sequences

23 Jun 2012; Justin Lecher (jlec) maq-0.7.1-r1.ebuild,
+files/maq-0.7.1-gcc-4.7.patch:
Add patch for gcc-4.7, #422869
alphaamd64armhppaia64ppcppc64sparcx86
0.7.1-r1 + +
0.7.1 + +
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sci-biology/maqview

*maqview-0.2.5-r2 (23 Jan 2013)
23 Jan 2013; Justin Lecher (jlec) +maqview-0.2.5-r2.ebuild,
+files/maqview-0.2.5-gcc4.7.patch, metadata.xml:
Fix compilation with gcc-4.7, #451438
alphaamd64armhppaia64ppcppc64sparcx86
0.2.5-r2
0.2.5-r1 + +
0.2.5 + +
sci-biology Homepages: ChangeLog Metadata Similar Bugs Forums

sci-biology/mauve

Multiple genome alignment with large-scale evolutionary events (GUI component)

09 Mar 2010; Jonathan Callen (abcd) mauve-9999.ebuild:
QA: Do not use absolute path to icon when in standard dirs (in
make_desktop_entry())
alphaamd64armhppaia64ppcppc64sparcx86
9999
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sci-biology/mauvealigner

Multiple genome alignment with large-scale evolutionary events (aligner component)

*mauvealigner-9999 (17 Apr 2009)
17 Apr 2009; Andrey Kislyuk (weaver) +metadata.xml,
+mauvealigner-9999.ebuild:
New package, ebuild written by me
alphaamd64armhppaia64ppcppc64sparcx86
9999
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sci-biology/mcl

A Markov Cluster Algorithm implementation

*mcl-12.135 (17 Feb 2013)
17 Feb 2013; Justin Lecher (jlec) mcl-08.312.ebuild,
+mcl-12.135.ebuild, metadata.xml:
Version BUmp; move to autotools-utils; install docs in right place, #296893
alphaamd64armhppaia64ppcppc64sparcx86
12.135 ~ ~
08.312 ~ ~
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sci-biology/meme

The MEME/MAST system - Motif discovery and search

19 Mar 2013; Justin Lecher (jlec) meme-4.8.1-r2.ebuild:
Fix renaming procedure, #460372
alphaamd64armhppaia64ppcppc64sparcx86
4.8.1-r2 + +
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sci-biology/mira

Whole Genome Shotgun and EST Sequence Assembler for Sanger, 454 and Solexa / Illumina

*mira-3.4.0.2 (07 Nov 2012)
07 Nov 2012; Justin Lecher (jlec) mira-3.2.1.ebuild,
mira-3.2.1-r1.ebuild, +mira-3.4.0.2.ebuild,
+files/mira-3.4.0.2-boost-1.50.patch:
Version Bump, #377807
alphaamd64armhppaia64ppcppc64sparcx86
3.4.0.2 ~ ~
3.2.1-r1 ~ ~
3.2.1 + +
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sci-biology/mosaik

A reference-guided aligner for next-generation sequencing technologies

*mosaik-1.0.1388 (11 Apr 2010)
11 Apr 2010; Andrey Kislyuk (weaver) +mosaik-1.0.1388.ebuild:
Version bump, address bug 314659
alphaamd64armhppaia64ppcppc64sparcx86
1.0.1388 ~ ~
1.0.1367 + +
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sci-biology/mothur

A suite of algorithms for ecological bioinformatics

*mothur-1.27.0 (14 Aug 2012)
*mothur-1.13.0-r2 (14 Aug 2012)
14 Aug 2012; Justin Lecher (jlec) mothur-1.6.0.ebuild,
mothur-1.13.0-r1.ebuild, +mothur-1.13.0-r2.ebuild,
+files/mothur-1.13.0-overflows2.patch, +mothur-1.27.0.ebuild,
+files/mothur-1.27.0-makefile.patch, +files/mothur-1.27.0-overflows.patch:
Version BUmp; fix for buffer overflows, #431258
alphaamd64armhppaia64ppcppc64sparcx86
1.27.0 ~ ~
1.13.0-r2 ~ ~
1.13.0-r1 ~ ~
1.6.0 + +
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sci-biology/mrbayes

Bayesian Inference of Phylogeny

21 Dec 2011; Pawel Hajdan jr (phajdan.jr) mrbayes-3.1.2-r1.ebuild:
x86 stable wrt bug #393969
alphaamd64armhppaia64ppcppc64sparcx86
3.1.2-r1 + +
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sci-biology/mummer

A rapid whole genome aligner

31 May 2011; Markus Meier (maekke) mummer-3.22-r1.ebuild:
x86 stable, bug #368341
alphaamd64armhppaia64ppcppc64sparcx86
3.22-r1 + +
3.21 + +
3.20 + +
sci-biology Homepage Artistic ChangeLog Metadata Similar Bugs Forums

sci-biology/muscle

Multiple sequence comparison by log-expectation

20 Jul 2010; Joseph Jezak (josejx) muscle-3.7-r1.ebuild:
Marked ppc stable for bug #277980.
alphaamd64armhppaia64ppcppc64sparcx86
3.8.31 ~ ~ ~
3.7-r1 + + +
3.7 + ~ ~
3.6 + + +
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sci-biology/ncbi-tools

03 Mar 2013; Agostino Sarubbo (ago) ncbi-tools-2.2.26-r2.ebuild:
Stable for ppc64, wrt bug #458112
alphaamd64armhppaia64ppcppc64sparcx86
2.2.26-r2
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sci-biology/ncbi-tools++

NCBI C++ Toolkit, including NCBI BLAST+

05 Nov 2012; Justin Lecher (jlec)
ncbi-tools++-0.2010.06.15-r1.ebuild:
Correct patch naming again
alphaamd64armhppaia64ppcppc64sparcx86
0.2010.06.15-r1 ~ ~
sci-biology Homepage public-domain ChangeLog Metadata Similar Bugs Forums

sci-biology/newick-utils

Tools for processing phylogenetic trees (re-root, subtrees, trimming, pruning, condensing, drawing)

13 Jul 2011; Kacper Kowalik (xarthisius)
newick-utils-1.3.0.ebuild, newick-utils-1.5.0.ebuild:
Add blocker for dev-games/libnw wrt #375059
alphaamd64armhppaia64ppcppc64sparcx86
1.5.0 ~ ~
1.3.0 + +
sci-biology Homepage BSD ChangeLog Metadata Similar Bugs Forums

sci-biology/njplot

A phylogenetic tree drawing program which supports tree rooting

31 Oct 2009; Markus Meier (maekke) njplot-2.3.ebuild:
amd64/x86 stable, bug #290935
alphaamd64armhppaia64ppcppc64sparcx86
2.3 + +
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sci-biology/pals

Pairwise Aligner for Long Sequences

22 Sep 2009; Markus Meier (maekke) pals-1.0.ebuild:
x86 stable, bug #283681
alphaamd64armhppaia64ppcppc64sparcx86
1.0 + +
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sci-biology/paml

Phylogenetic Analysis by Maximum Likelihood

12 Sep 2010; Markos Chandras (hwoarang) paml-4.4c.ebuild:
Stable on amd64 wrt bug #335649
alphaamd64armhppaia64ppcppc64sparcx86
4.4c + +
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sci-biology/phrap

Phrap, swat, cross_match: Shotgun assembly and alignment utilities

17 Feb 2013; Justin Lecher (jlec) phrap-1.080812.ebuild,
metadata.xml:
Add missing deps, thanks Martin Mokrejš for the patch
alphaamd64armhppaia64ppcppc64sparcx86
1.080812 ~ ~
sci-biology Homepage phrap ChangeLog Metadata Similar Bugs Forums

sci-biology/phred

A base caller for Sanger DNA sequencing

07 Jul 2009; Diego E. Pettenò (flameeyes) phred-071220.ebuild:
Use elog for fetch error.
alphaamd64armhppaia64ppcppc64sparcx86
071220 ~ ~
sci-biology Homepage phrap ChangeLog Metadata Similar Bugs Forums

sci-biology/phylip

*phylip-3.69-r1 (17 Feb 2013)
17 Feb 2013; Justin Lecher (jlec) -phylip-3.68.ebuild,
+phylip-3.69-r1.ebuild, metadata.xml:
Respect LDFLAGS, #337921
alphaamd64armhppaia64ppcppc64sparcx86
3.69-r1
3.69 + ~ +
3.67 + + +
sci-biology Homepages: ChangeLog Metadata Similar Bugs Forums

sci-biology/phyml

Estimation of large phylogenies by maximum likelihood

17 Feb 2013; Agostino Sarubbo (ago) phyml-2.4.5-r2.ebuild:
Stable for x86, wrt bug #328425
alphaamd64armhppaia64ppcppc64sparcx86
2.4.5-r2 + ~ +
sci-biology Homepage GPL-2 ChangeLog Metadata Similar Bugs Forums

sci-biology/picard

Java-based command-line utilities that manipulate SAM files

*picard-1.63 (28 Feb 2012)
28 Feb 2012; Andrey Kislyuk (weaver) +picard-1.63.ebuild:
Version bump
alphaamd64armhppaia64ppcppc64sparcx86
1.63 M~
1.58 M~
sci-biology Homepage Apache-2.0 ChangeLog Metadata Similar Bugs Forums

sci-biology/piler

Analysis of repetitive DNA found in genome sequences

22 Sep 2009; Markus Meier (maekke) piler-1.0.ebuild:
x86 stable, bug #283683
alphaamd64armhppaia64ppcppc64sparcx86
1.0 + +
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sci-biology/pilercr

Analysis of Clustered Regularly Interspaced Short Palindromic Repeats (CRISPRs)

26 Apr 2012; Justin Lecher (jlec) pilercr-1.0.ebuild:
Move to EAPI=, remove unecessary die
alphaamd64armhppaia64ppcppc64sparcx86
1.0 + +
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sci-biology/plink

Whole genome association analysis toolset

27 Feb 2013; Justin Lecher (jlec) files/1.07-flags.patch,
plink-1.07-r1.ebuild, metadata.xml:
Use detected pkg-config instead of generic
alphaamd64armhppaia64ppcppc64sparcx86
1.07-r1 + +
1.07 + +
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sci-biology/poa

Fast multiple sequence alignments using partial-order graphs

*poa-2-r1 (18 Sep 2010)
18 Sep 2010; Justin Lecher (jlec) +files/2-respect-flags.patch,
+poa-2-r1.ebuild:
Respecting LDFLAGS, 337856
alphaamd64armhppaia64ppcppc64sparcx86
2-r1 ~ ~
2 ~ ~
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sci-biology/prank

Probabilistic Alignment Kit

20 Jun 2012; Justin Lecher (jlec) prank-100701.ebuild,
prank-111130.ebuild, +files/prank-111130-gcc-4.7.patch:
Fix compilation with gcc-4.7, #422581
alphaamd64armhppaia64ppcppc64sparcx86
111130 ~ ~
100701 ~ ~
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sci-biology/primer3

*primer3-2.3.5 (14 Feb 2013)
14 Feb 2013; Justin Lecher (jlec) +primer3-2.3.5.ebuild:
Version Bump
alphaamd64armhppaia64ppcppc64sparcx86
2.3.5
2.3.4 ~ ~ ~ ~ ~
2.3.1 + + ~ ~ +
sci-biology Homepages: ChangeLog Metadata Similar Bugs Forums

sci-biology/prints

A protein motif fingerprint database

07 Mar 2012; Brent Baude (ranger) prints-39.0.ebuild:
Marking prints-39.0 ppc for bug 393929
alphaamd64armhppaia64ppcppc64sparcx86
39.0 + + +
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sci-biology/probcons

Probabilistic Consistency-based Multiple Alignment of Amino Acid Sequences

13 Jun 2011; Justin Lecher (jlec) probcons-1.12-r1.ebuild,
+files/probcons-1.12-gcc-4.6.patch:
Make it gcc46 resistant, #370471
alphaamd64armhppaia64ppcppc64sparcx86
1.12-r1 + +
1.12 ~ ~
1.10 +
sci-biology Homepage public-domain ChangeLog Metadata Similar Bugs Forums

sci-biology/prodigal

Prokaryotic Dynamic Programming Genefinding Algorithm

*prodigal-2.60 (02 Jan 2012)
02 Jan 2012; Andrey Kislyuk (weaver) +prodigal-2.60.ebuild:
Version bump
alphaamd64armhppaia64ppcppc64sparcx86
2.60 ~
2.50 ~
sci-biology Homepages: 1 2 GPL-3 ChangeLog Metadata Similar Bugs Forums

sci-biology/profphd

Secondary structure and solvent accessibility predictor

24 Apr 2013; Justin Lecher (jlec) profphd-1.0.39.ebuild:
Updated deps
alphaamd64armhppaia64ppcppc64sparcx86
1.0.39 ~ ~
sci-biology Homepage GPL-2 ChangeLog Metadata Similar Bugs Forums

sci-biology/prosite

A protein families and domains database

13 Dec 2011; Agostino Sarubbo (ago) prosite-20.72.ebuild:
Stable for AMD64, wrt bug #392825
alphaamd64armhppaia64ppcppc64sparcx86
20.72 + ~ +
20.52 ~ ~ ~
20.36 + ~ +
19.36 + + +
sci-biology Homepage swiss-prot ChangeLog Metadata Similar Bugs Forums

sci-biology/psipred

Protein Secondary Structure Prediction

11 Jul 2012; Justin Lecher (jlec) psipred-3.2.1.ebuild:
Cleaned SRC_URI
alphaamd64armhppaia64ppcppc64sparcx86
3.3 ~ ~
3.2.1 ~ ~
3.2 ~ ~
3.1 ~ ~
sci-biology Homepage psipred ChangeLog Metadata Similar Bugs Forums

sci-biology/pysam

Python interface for the SAM/BAM sequence alignment and mapping format

25 Feb 2012; Patrick Lauer (patrick) pysam-0.6.ebuild:
Restricting py 2.5, pypy and jython
alphaamd64armhppaia64ppcppc64sparcx86
0.6 ~
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sci-biology/qrna

Prototype ncRNA genefinder

06 Dec 2012; Pawel Hajdan jr (phajdan.jr) qrna-2.0.3c-r1.ebuild:
x86 stable wrt bug #441020
alphaamd64armhppaia64ppcppc64sparcx86
2.0.3c-r1 + ~ +
sci-biology Homepage GPL-2 ChangeLog Metadata Similar Bugs Forums

sci-biology/raxml

A Program for Sequential, Parallel & Distributed Inference of Large Phylogenetic Trees

18 Feb 2013; Justin Lecher (jlec) -raxml-7.2.2.ebuild,
-raxml-7.2.5.ebuild, -raxml-7.2.5-r1.ebuild, raxml-7.2.6.ebuild,
metadata.xml:
Drop old; stop building when non sse3 capable CPU is detected, #375061
alphaamd64armhppaia64ppcppc64sparcx86
7.2.6 ~ ~
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sci-biology/readseq

Reads and writes nucleic/protein sequences in various formats.

01 Feb 2013; Justin Lecher (jlec) -readseq-19930201.ebuild,
-readseq-19930201-r1.ebuild, readseq-20080420.ebuild, metadata.xml:
Drop old; Resolve file collision sci-biology/meme, #455010
alphaamd64armhppaia64ppcppc64sparcx86
20080420 ~ ~
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sci-biology/rebase

*rebase-1303 (28 Feb 2013)
28 Feb 2013; Justin Lecher (jlec) +rebase-1303.ebuild,
metadata.xml:
Version Bump
alphaamd64armhppaia64ppcppc64sparcx86
1303
1202 ~ ~ ~
1111 + + +
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sci-biology/recon

Automated de novo identification of repeat families from genomic sequences

*recon-1.06-r2 (26 Aug 2012)
26 Aug 2012; Justin Lecher (jlec) +recon-1.06-r2.ebuild,
+files/recon-1.06-respect.patch:
Respect CFLAGS and CC, #432660
alphaamd64armhppaia64ppcppc64sparcx86
1.06-r2 ~ ~
1.06-r1 ~ ~
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sci-biology/repeatmasker

*repeatmasker-4.0.1 (07 Mar 2013)
07 Mar 2013; Justin Lecher (jlec) -repeatmasker-3.2.7.ebuild,
-repeatmasker-3.2.8.ebuild, -repeatmasker-3.2.9.ebuild,
+repeatmasker-4.0.1.ebuild, metadata.xml:
Version BUmp; cleaned old
alphaamd64armhppaia64ppcppc64sparcx86
4.0.1
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sci-biology/repeatmasker-libraries

*repeatmasker-libraries-20120418 (07 Mar 2013)
07 Mar 2013; Justin Lecher (jlec)
-repeatmasker-libraries-20090120.ebuild,
-repeatmasker-libraries-20090604.ebuild,
+repeatmasker-libraries-20120418.ebuild, metadata.xml:
Version BUmp; cleaned old; fix license
alphaamd64armhppaia64ppcppc64sparcx86
20120418
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sci-biology/rmblast

*rmblast-1.2-r1 (18 Feb 2013)
18 Feb 2013; Justin Lecher (jlec) rmblast-1.2.ebuild,
+rmblast-1.2-r1.ebuild, +files/rmblast-1.2-gcc47.patch, metadata.xml:
Bug fixes: Build against any boost, #356315; build with gcc-4.7, #442266
alphaamd64armhppaia64ppcppc64sparcx86
1.2-r1
1.2 ~ ~
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sci-biology/rnaview

Generates 2D displays of RNA/DNA secondary structures with tertiary interactions

*rnaview-20040713-r3 (03 Aug 2012)
03 Aug 2012; Justin Lecher (jlec) +rnaview-20040713-r3.ebuild,
files/rnaview-20040713-makefile.patch:
Respect CFLAGS, #429536; Bump to EAPI=4
alphaamd64armhppaia64ppcppc64sparcx86
20040713-r3 ~ ~
20040713-r2 ~ ~
20040713 ~ +
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sci-biology/samtools

*samtools-0.1.18-r3 (29 Mar 2013)
29 Mar 2013; Justin Lecher (jlec) +samtools-0.1.18-r3.ebuild:
Install bcftools and vcfutils.pl pointed out by mahnmut
alphaamd64armhppaia64ppcppc64sparcx86
0.1.18-r3
0.1.18-r2
0.1.18 ~ ~
0.1.12 + +
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sci-biology/seaview

A graphical multiple sequence alignment editor

10 Dec 2012; Agostino Sarubbo (ago) seaview-4.3.5.ebuild:
Add ~ppc, wrt bug #432368
alphaamd64armhppaia64ppcppc64sparcx86
4.3.5 ~ ~ ~
4.3.3 + +
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sci-biology/seqan

*seqan-1.3.1-r1 (29 Mar 2013)
29 Mar 2013; Justin Lecher (jlec) -seqan-1.3.1.ebuild,
+seqan-1.3.1-r1.ebuild:
Correct doc installation path
alphaamd64armhppaia64ppcppc64sparcx86
1.3.1-r1
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sci-biology/shrimp

17 Feb 2013; Justin Lecher (jlec) shrimp-2.2.3.ebuild:
Force sse2 support by the cpu, #337401
alphaamd64armhppaia64ppcppc64sparcx86
2.2.3
2.0.1 + +
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sci-biology/sibsim4

17 Feb 2013; Agostino Sarubbo (ago) sibsim4-0.20.ebuild:
Stable for amd64, wrt bug #328431
alphaamd64armhppaia64ppcppc64sparcx86
0.20
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sci-biology/sim4

A program to align cDNA and genomic DNA

*sim4-20030921-r1 (01 Sep 2010)
01 Sep 2010; Kacper Kowalik (xarthisius)
+sim4-20030921-r1.ebuild:
Respect CC,CFLAGS,LDFLAGS wrt bug 335553. Thanks to Diego for the report.
alphaamd64armhppaia64ppcppc64sparcx86
20030921-r1 ~ ~ ~
20030921 ~ +
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sci-biology/snpfile

A library and API for manipulating large SNP datasets

15 Jan 2012; Pawel Hajdan jr (phajdan.jr) snpfile-2.0.1-r1.ebuild:
x86 stable wrt bug #326455
alphaamd64armhppaia64ppcppc64sparcx86
2.0.1-r1 + +
2.0.1 + +
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sci-biology/stride

Protein secondary structure assignment from atomic coordinates

14 Apr 2013; Justin Lecher (jlec) stride-20011129.ebuild,
stride-20011129-r1.ebuild, metadata.xml:
Fix license, thanks ulm looking for correct licensing
alphaamd64armhppaia64ppcppc64sparcx86
20011129-r1 ~ ~ ~
20011129 ~ ~ ~
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sci-biology/t-coffee

03 Feb 2013; Agostino Sarubbo (ago) t-coffee-9.03.1318-r1.ebuild:
Add ~ppc, wrt bug #452010
alphaamd64armhppaia64ppcppc64sparcx86
9.03.1318-r1
8.93 ~ ~ ~
8.69 + + +
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sci-biology/tophat

*tophat-2.0.8 (13 Mar 2013)
13 Mar 2013; Justin Lecher (jlec) +tophat-2.0.8.ebuild,
+files/tophat-2.0.8-flags.patch:
Version Bump; unbundle sci-biology/seqan
alphaamd64armhppaia64ppcppc64sparcx86
2.0.8
2.0.2 ~ ~
2.0.0 ~ ~
1.4.1 ~ ~
1.0.12 + +
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sci-biology/transfac

A database of eucaryotic transcription factors

09 Aug 2011; Kacper Kowalik (xarthisius) transfac-3.2.ebuild:
ppc64 keyword dropped
alphaamd64armhppaia64ppcppc64sparcx86
3.2 + + +
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sci-biology/tree-puzzle

Maximum likelihood analysis for nucleotide, amino acid, and two-state data

01 Aug 2012; Justin Lecher (jlec) tree-puzzle-5.2.ebuild,
+files/tree-puzzle-impl-dec.patch:
Mask stupid test, which fails due to precision reached depending on
optimization used at compile time, #297646; fix move to EAPI=4, #429354
alphaamd64armhppaia64ppcppc64sparcx86
5.2 ~ ~ +
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sci-biology/treeviewx

A phylogenetic tree viewer

12 Oct 2010; Pawel Hajdan jr (phajdan.jr)
treeviewx-0.5.1-r2.ebuild:
x86 stable wrt bug #340471
alphaamd64armhppaia64ppcppc64sparcx86
0.5.1-r2 + +
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sci-biology/trf

Tandem Repeats Finder

04 Mar 2013; Justin Lecher (jlec) trf-4.04.ebuild, metadata.xml:
What happens in /opt, stays in /opt
alphaamd64armhppaia64ppcppc64sparcx86
4.04 + +
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sci-biology/trnascan-se

tRNA detection in large-scale genome sequences

16 Jul 2010; Markos Chandras (hwoarang)
trnascan-se-1.23-r2.ebuild:
Stable on amd64 wrt bug #328435
alphaamd64armhppaia64ppcppc64sparcx86
1.23-r2 + +
1.23-r1 ~ +
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sci-biology/uchime

Fast, accurate chimera detection

*uchime-4.2.40 (14 Aug 2012)
14 Aug 2012; Justin Lecher (jlec) +uchime-4.2.40.ebuild,
+files/CMakeLists.txt, +metadata.xml:
New addition
alphaamd64armhppaia64ppcppc64sparcx86
4.2.40 ~ ~
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sci-biology/ucsc-genome-browser

The UCSC genome browser suite, also known as Jim Kent's library and GoldenPath

*ucsc-genome-browser-260 (27 Dec 2011)
27 Dec 2011; Justin Lecher (jlec) +ucsc-genome-browser-260.ebuild,
metadata.xml:
Version Bump, move to EAPI=4, handled static-libs, respect mostly everywhere
LDFALGS
alphaamd64armhppaia64ppcppc64sparcx86
260 ~ ~
223 ~ ~
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sci-biology/unafold

*unafold-3.8-r1 (18 Feb 2013)
18 Feb 2013; Justin Lecher (jlec) unafold-3.8.ebuild,
+unafold-3.8-r1.ebuild, metadata.xml:
Fix test, #358053; respect CFLAGS
alphaamd64armhppaia64ppcppc64sparcx86
3.8-r1
3.8 ~ ~
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sci-biology/vaal

*vaal-45166 (20 Feb 2013)
20 Feb 2013; Justin Lecher (jlec) +vaal-45166.ebuild,
metadata.xml:
Version BUmp
alphaamd64armhppaia64ppcppc64sparcx86
45166
42179 ~ ~
1.6 + ~
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sci-biology/vcftools

Tools for working with VCF (Variant Call Format) files

27 Feb 2013; Justin Lecher (jlec) vcftools-0.1.8.ebuild,
files/vcftools-0.1.8-buildsystem.patch, metadata.xml:
Use PKG_CONFIG instead of generic pkg-config
alphaamd64armhppaia64ppcppc64sparcx86
0.1.8 ~ ~
0.1.7 ~ ~
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sci-biology/velvet

A sequence assembler for very short reads

21 Dec 2011; Justin Lecher (jlec) -velvet-0.7.55.ebuild,
-velvet-0.7.62.ebuild:
Cleaned old
alphaamd64armhppaia64ppcppc64sparcx86
1.0.18-r1 + +
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sci-biology/vienna-rna

*vienna-rna-2.1.1 (13 Feb 2013)
13 Feb 2013; Justin Lecher (jlec) +vienna-rna-2.1.1.ebuild,
+files/vienna-rna-2.1.1-bindir.patch,
+files/vienna-rna-2.1.1-impl-decl.patch, +files/vienna-rna-2.1.1-prll.patch,
+files/vienna-rna-2.1.1-setup.py:
Version Bump; move to EAPI=5, new python eclasses; autotools-utils
alphaamd64armhppaia64ppcppc64sparcx86
2.1.1
1.8.5 + + +
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sci-biology/wgs-assembler

A de novo whole-genome shotgun DNA sequence assembler, also known as the Celera Assembler and CABOG

14 Nov 2012; Andreas Schuerch (nativemad)
wgs-assembler-7.0-r1.ebuild:
x86 stable, see bug 328437
alphaamd64armhppaia64ppcppc64sparcx86
7.0-r1 + +
7.0 ~ ~
6.1 ~ +
5.4 + +
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sci-biology/wise

Intelligent algorithms for DNA searches

02 Oct 2010; Andreas K. Huettel (dilfridge) wise-2.2.0.ebuild,
wise-2.4.0_alpha.ebuild:
Less strict RDEPEND: ~sci-biology/hmmer-2.3.2 instead of
=sci-biology/hmmer-2.3.2-r1. Fixes bug 265534.
alphaamd64armhppaia64ppcppc64sparcx86
2.4.0_alpha ~ ~ ~ ~ ~
2.2.0 ~ ~ + ~ +
sci-biology Homepage BSD ChangeLog Metadata Similar Bugs Forums

sci-biology/yass

Genomic similarity search with multiple transition constrained spaced seeds

*yass-1.14-r1 (21 Jun 2010)
21 Jun 2010; Justin Lecher (jlec) +files/1.14-as-needed.patch,
+yass-1.14-r1.ebuild:
As-needed fix 324945, added threads and lowmem USE
alphaamd64armhppaia64ppcppc64sparcx86
1.14-r1 ~ ~
1.14 ~ ~
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Last update:
26 May 2013
09:01 UTC

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