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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

06 Jul 2014; Justin Lecher (jlec) abyss-1.3.6.ebuild:
Add missing dep on boost, #515156
alphaamd64armhppaia64ppcppc64sparcx86
1.3.6 ~ ~
1.3.4 ~ ~
1.3.3 + +
sci-biology Homepage abyss ChangeLog Metadata Similar Bugs Forums

sci-biology/allpathslg

De novo assembly of whole-genome shotgun microreads

*allpathslg-52415 (31 Mar 2015)
31 Mar 2015; Justin Lecher (jlec) +allpathslg-52415.ebuild:
Version BUmp; move to EAPI=5 and autotools-utils.eclass; thanks Martin Mokrejs
for preparing the bump
alphaamd64armhppaia64ppcppc64sparcx86
52415 ~
47093 ~ -
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

08 Apr 2015; Michał Górny (mgorny) amos-3.1.0-r1.ebuild:
Drop old Python implementations
alphaamd64armhppaia64ppcppc64sparcx86
3.1.0-r1 ~ ~
3.1.0 + +
sci-biology Homepage Artistic ChangeLog Metadata Similar Bugs Forums

sci-biology/ApE

A Plasmid Editor

20 Mar 2015; Justin Lecher (jlec) -ApE-2.0.7.ebuild,
ApE-2.0.7-r1.ebuild, metadata.xml:
Fix tcl/tk slotting;drop old; Bump EAPI
alphaamd64armhppaia64ppcppc64sparcx86
2.0.7-r1 ~ ~
sci-biology Homepage ApE ChangeLog Metadata Similar Bugs Forums

sci-biology/arb

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

11 Mar 2013; Justin Lecher (jlec) metadata.xml:
Drop Andrey as maintainer so that bugs get assigned to sci-biology directly
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

11 Mar 2013; Justin Lecher (jlec) metadata.xml:
Drop Andrey as maintainer so that bugs get assigned to sci-biology directly
alphaamd64armhppaia64ppcppc64sparcx86
2.5.5 + +
sci-biology Homepage Artistic ChangeLog Metadata Similar Bugs Forums

sci-biology/bamtools

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

*bamtools-2.3.0 (17 Sep 2013)
17 Sep 2013; Justin Lecher (jlec) -bamtools-2.2.3.ebuild,
+bamtools-2.3.0.ebuild, +files/bamtools-2.3.0-unbundle.patch:
Version Bump, drop old, #482636; thanks Martin Mokrejš for the patch
alphaamd64armhppaia64ppcppc64sparcx86
2.3.0 ~ ~
1.0.2 ~ ~
sci-biology Homepage MIT ChangeLog Metadata Similar Bugs Forums

sci-biology/beast-mcmc

Bayesian MCMC of Evolution & Phylogenetics using Molecular Sequences

11 Mar 2013; Justin Lecher (jlec) metadata.xml:
Drop Andrey as maintainer so that bugs get assigned to sci-biology directly
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-2.20.1 (30 May 2014)
30 May 2014; Sven Vermeulen (swift) +bedtools-2.20.1.ebuild:
Add bedtools 2.20.1 thanks to Martin Mokrejs (bug #505538)
alphaamd64armhppaia64ppcppc64sparcx86
2.20.1 ~ ~
2.16.2 ~ ~
sci-biology Homepage GPL-2 ChangeLog Metadata Similar Bugs Forums

sci-biology/bfast

Blat-like Fast Accurate Search Tool

11 Mar 2013; Justin Lecher (jlec) metadata.xml:
Drop Andrey as maintainer so that bugs get assigned to sci-biology directly
alphaamd64armhppaia64ppcppc64sparcx86
0.7.0a ~ ~
sci-biology Homepage GPL-2 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 ~ ~
sci-biology Homepage GPL-2 ChangeLog Metadata Similar Bugs Forums

sci-biology/bioperl

Perl tools for bioinformatics - Core modules

27 May 2015; Agostino Sarubbo (ago) bioperl-1.6.9.ebuild:
Stable for amd64, wrt bug #539426
alphaamd64armhppaia64ppcppc64sparcx86
9999-r1
1.6.9 + +
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

27 May 2015; Agostino Sarubbo (ago) bioperl-db-1.6.9.ebuild:
Stable for amd64, wrt bug #539426
alphaamd64armhppaia64ppcppc64sparcx86
9999-r1
1.6.9 + +
sci-biology Homepage Artistic GPL-2 ChangeLog Metadata Similar Bugs Forums

sci-biology/bioperl-network

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

27 May 2015; Agostino Sarubbo (ago) bioperl-network-1.6.9.ebuild:
Stable for amd64, wrt bug #539426
alphaamd64armhppaia64ppcppc64sparcx86
9999-r1
1.6.9 + +
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sci-biology/bioperl-run

Perl tools for bioinformatics - Wrapper modules around key bioinformatics applications

27 May 2015; Agostino Sarubbo (ago) bioperl-run-1.6.9.ebuild:
Stable for amd64, wrt bug #539426
alphaamd64armhppaia64ppcppc64sparcx86
9999-r1
1.6.9 + +
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sci-biology/biopython

Python modules for computational molecular biology

28 Mar 2015; Agostino Sarubbo (ago) biopython-1.65.ebuild:
Stable for ppc, wrt bug #544544
alphaamd64armhppaia64ppcppc64sparcx86
1.65 + + +
sci-biology Homepages: 1 2 HPND ChangeLog Metadata Similar Bugs Forums

sci-biology/bioruby

An integrated environment for bioinformatics using the Ruby language

07 May 2014; Manuel Rüger (mrueg) bioruby-1.4.3.0001-r1.ebuild,
bioruby-9999.ebuild:
Remove ruby18 target.
alphaamd64armhppaia64ppcppc64sparcx86
9999
1.4.3.0001-r1 + ~ +
sci-biology Homepage Ruby ChangeLog Metadata Similar Bugs Forums

sci-biology/biosql

A generic bioinformatics relational database model

11 Mar 2013; Justin Lecher (jlec) metadata.xml:
Drop Andrey as maintainer so that bugs get assigned to sci-biology directly
alphaamd64armhppaia64ppcppc64sparcx86
1.0.1 + +
sci-biology Homepage LGPL-3 ChangeLog Metadata Similar Bugs Forums

sci-biology/blat

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

11 Mar 2013; Justin Lecher (jlec) metadata.xml:
Drop Andrey as maintainer so that bugs get assigned to sci-biology directly
alphaamd64armhppaia64ppcppc64sparcx86
34-r1 ~ ~
34 + +
sci-biology Homepage blat ChangeLog Metadata Similar Bugs Forums

sci-biology/blossoc

A linkage disequilibrium association mapping tool

11 Mar 2013; Justin Lecher (jlec) metadata.xml:
Drop Andrey as maintainer so that bugs get assigned to sci-biology directly
alphaamd64armhppaia64ppcppc64sparcx86
1.4.0 + +
sci-biology Homepage GPL-3 ChangeLog Metadata Similar Bugs Forums

sci-biology/bowtie

An ultrafast memory-efficient short read aligner

18 Sep 2013; Justin Lecher (jlec) bowtie-1.0.0.ebuild:
Fix location of html files, #484620
alphaamd64armhppaia64ppcppc64sparcx86
1.0.0 ~ ~
0.12.8 + +
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sci-biology/bwa

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

19 Apr 2015; Agostino Sarubbo (ago) bwa-0.7.12.ebuild:
Stable for x86, wrt bug #544944
alphaamd64armhppaia64ppcppc64sparcx86
0.7.12 + +
sci-biology Homepage GPL-3 ChangeLog Metadata Similar Bugs Forums

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 ~ ~
sci-biology Homepage GPL-2 ChangeLog Metadata Similar Bugs Forums

sci-biology/clustal-omega

Scalable multiple alignment of protein sequences

*clustal-omega-1.2.1 (28 Mar 2015)
28 Mar 2015; Justin Lecher (jlec) +clustal-omega-1.2.1.ebuild,
-clustal-omega-1.0.3.ebuild, -clustal-omega-1.1.0.ebuild:
Version BUmp; drop old
alphaamd64armhppaia64ppcppc64sparcx86
1.2.1 ~ ~
1.2.0 ~ ~
sci-biology Homepage GPL-2 ChangeLog Metadata Similar Bugs Forums

sci-biology/clustalw

General purpose multiple alignment program for DNA and proteins

26 Jan 2014; Agostino Sarubbo (ago) clustalw-1.83-r3.ebuild:
Stable for sparc, wrt bug #497214
alphaamd64armhppaia64ppcppc64sparcx86
2.1 + +
1.83-r3 + + + + + +
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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

19 Apr 2015; Agostino Sarubbo (ago) clustalx-2.1-r1.ebuild:
Stable for x86, wrt bug #544936
alphaamd64armhppaia64ppcppc64sparcx86
2.1-r1 + +
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sci-biology/consed

A genome sequence finishing program

*consed-27 (26 Oct 2014)
26 Oct 2014; Justin Lecher (jlec) -consed-19-r1.ebuild,
+consed-27.ebuild:
Import to tree; drop old EPAI=1 version, #526742
alphaamd64armhppaia64ppcppc64sparcx86
27 ~ ~
19-r2 ~ ~
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sci-biology/cufflinks

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

17 Feb 2015; Justin Lecher (jlec) cufflinks-2.2.1-r1.ebuild:
Drop missing patch
alphaamd64armhppaia64ppcppc64sparcx86
2.2.1-r1 ~ ~
2.2.1 ~ ~
1.3.0-r1 ~ ~
sci-biology Homepage Artistic ChangeLog Metadata Similar Bugs Forums

sci-biology/cutg

Codon usage tables calculated from GenBank

28 Mar 2015; Agostino Sarubbo (ago) cutg-160-r1.ebuild:
Stable for ppc, wrt bug #542246
alphaamd64armhppaia64ppcppc64sparcx86
160-r1 + + +
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sci-biology/dialign-tx

Greedy and progressive approaches for segment-based multiple sequence alignment

20 Apr 2015; Justin Lecher (jlec) -dialign-tx-1.0.2.ebuild,
dialign-tx-1.0.2-r1.ebuild:
Drop old
alphaamd64armhppaia64ppcppc64sparcx86
1.0.2-r1 + +
sci-biology Homepage LGPL-2.1 ChangeLog Metadata Similar Bugs Forums

sci-biology/dialign2

Multiple sequence alignment

*dialign2-2.2.1 (29 Mar 2015)
29 Mar 2015; Justin Lecher (jlec) +dialign2-2.2.1.ebuild,
+metadata.xml:
New addition written by me
alphaamd64armhppaia64ppcppc64sparcx86
2.2.1 ~ ~
sci-biology Homepage LGPL-2.1 ChangeLog Metadata Similar Bugs Forums

sci-biology/diya

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

15 Jul 2014; Mikle Kolyada (zlogene) diya-1.0_rc4.ebuild:
Bump to EAPI=5
alphaamd64armhppaia64ppcppc64sparcx86
1.0_rc4 ~ ~
sci-biology Homepage GPL-3 ChangeLog Metadata Similar Bugs Forums

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 +
sci-biology Homepage Artistic ChangeLog Metadata Similar Bugs Forums

sci-biology/embassy

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

28 Mar 2015; Justin Lecher (jlec) -embassy-6.1.0.ebuild:
Drop old
alphaamd64armhppaia64ppcppc64sparcx86
6.6.0 ~ ~
6.0.1 + ~ +
sci-biology Homepage freedist ChangeLog Metadata Similar Bugs Forums

sci-biology/embassy-cbstools

EMBOSS integrated version of Applications from the CBS group

alphaamd64armhppaia64ppcppc64sparcx86
1.0.0.650 ~ ~ ~
1.0.0 + ~ +
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sci-biology/embassy-clustalomega

EMBOSS integrated version of Clustal Omega - Scalable multiple protein sequences alignment

28 Mar 2015; Justin Lecher (jlec)
embassy-clustalomega-1.1.0.ebuild:
Clean global scope
alphaamd64armhppaia64ppcppc64sparcx86
1.1.0 ~ ~
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sci-biology/embassy-domainatrix

EMBOSS integrated version of Protein domain analysis add-on package

alphaamd64armhppaia64ppcppc64sparcx86
0.1.650 ~ ~ ~
0.1.0-r3 + ~ +
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sci-biology/embassy-domalign

EMBOSS integrated version of Protein domain alignment add-on package

28 Mar 2015; Justin Lecher (jlec) embassy-domalign-0.1.650.ebuild:
Drop old
alphaamd64armhppaia64ppcppc64sparcx86
0.1.650 ~ ~ ~
0.1.0-r3 + ~ +
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sci-biology/embassy-domsearch

EMBOSS integrated version of Protein domain search add-on package

alphaamd64armhppaia64ppcppc64sparcx86
0.1.650 ~ ~ ~
0.1.0-r3 + ~ +
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sci-biology/embassy-emnu

EMBOSS integrated version of Simple menu of EMBOSS applications

28 Mar 2015; Justin Lecher (jlec) -embassy-emnu-1.05-r6.ebuild,
embassy-emnu-1.05.650.ebuild:
Drop old
alphaamd64armhppaia64ppcppc64sparcx86
1.05.650 ~ ~ ~
1.05-r5 + ~ +
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sci-biology/embassy-esim4

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

alphaamd64armhppaia64ppcppc64sparcx86
1.0.0.650 ~ ~ ~
1.0.0-r5 + ~ +
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sci-biology/embassy-hmmer

EMBOSS integrated version of Wrappers for HMMER - Biological sequence analysis with profile HMMs

alphaamd64armhppaia64ppcppc64sparcx86
2.3.2.650 ~ ~ ~
2.3.2-r2 + ~ +
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sci-biology/embassy-iprscan

EMBOSS integrated version of InterProScan motif detection add-on package

alphaamd64armhppaia64ppcppc64sparcx86
4.3.1.650 ~ ~ ~
4.3.1 + ~ +
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sci-biology/embassy-meme

EMBOSS integrated version of Wrappers for MEME - Multiple Em for Motif Elicitation

28 Mar 2015; Justin Lecher (jlec) embassy-meme-4.7.650.ebuild:
Clean global scope
alphaamd64armhppaia64ppcppc64sparcx86
4.7.650 ~ ~
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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
0.1.0-r1 + ~ +
sci-biology Homepage LGPL-2 GPL-2 ChangeLog Metadata Similar Bugs Forums

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 + ~ +
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sci-biology/embassy-mse

EMBOSS integrated version of MSE - Multiple Sequence Screen Editor

28 Mar 2015; Justin Lecher (jlec) -embassy-mse-1.0.0-r7.ebuild,
embassy-mse-3.0.0.650.ebuild:
Drop old
alphaamd64armhppaia64ppcppc64sparcx86
3.0.0.650 ~ ~ ~
1.0.0-r6 + ~ +
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sci-biology/embassy-phylipnew

EMBOSS integrated version of The Phylogeny Inference Package

alphaamd64armhppaia64ppcppc64sparcx86
3.69.650 ~ ~ ~
3.67 + ~ +
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sci-biology/embassy-signature

EMBOSS integrated version of Protein signature add-on package

*embassy-signature-0.1.650 (28 Mar 2015)
28 Mar 2015; Justin Lecher (jlec)
+embassy-signature-0.1.650.ebuild,
+files/embassy-signature-0.1.650_fix-build-system.patch, metadata.xml:
Import latest changes from science overlay, thanks Ted Tanberry for the work;
fixes #335603
alphaamd64armhppaia64ppcppc64sparcx86
0.1.650 ~ ~ ~
0.1.0-r3 + ~ +
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sci-biology/embassy-structure

EMBOSS integrated version of Protein structure add-on package

alphaamd64armhppaia64ppcppc64sparcx86
0.1.650 ~ ~ ~
0.1.0-r3 + ~ +
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sci-biology/embassy-topo

EMBOSS integrated version of Transmembrane protein display

28 Mar 2015; Justin Lecher (jlec) -embassy-topo-1.0.0-r6.ebuild,
embassy-topo-2.0.650.ebuild:
Drop old
alphaamd64armhppaia64ppcppc64sparcx86
2.0.650 ~ ~ ~
1.0.0-r5 + ~ +
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sci-biology/embassy-vienna

EMBOSS integrated version of Vienna RNA package - RNA folding

alphaamd64armhppaia64ppcppc64sparcx86
1.7.2.650 ~ ~ ~
1.7.2 + ~ +
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sci-biology/emboss

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

07 May 2015; Justin Lecher (jlec) emboss-6.6.0.ebuild,
files/emboss-6.6.0_fix-build-system.patch:
Correct Licenses, bug #548810; make build with newer plplot, bug #548806; add
missing dep, bug #544516
alphaamd64armhppaia64ppcppc64sparcx86
6.6.0 ~ ~ ~
6.3.1_p4-r1 ~ ~ ~
6.0.1 + + +
sci-biology Homepage LGPL-2 GPL-2 Apache-2.0 GPL-3+ CC-BY-3.0 ChangeLog Metadata Similar Bugs Forums

sci-biology/eugene

Eukaryotic gene predictor

25 Mar 2015; Agostino Sarubbo (ago) eugene-4.1.ebuild:
Stable for x86, wrt bug #543936
alphaamd64armhppaia64ppcppc64sparcx86
4.1 + +
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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 ~ ~
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sci-biology/express

Streaming RNA-Seq Analysis

*express-1.5.1 (13 Oct 2014)
13 Oct 2014; Justin Lecher (jlec) +express-1.5.1.ebuild,
+files/express-1.5.1-buildsystem.patch:
Version BUmp; thanks Michael Schubert for the initial patch, #525188
alphaamd64armhppaia64ppcppc64sparcx86
1.5.1 ~ ~
0.9.5-r1 ~ ~
0.9.5 ~ ~
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sci-biology/fasta

FASTA is a DNA and Protein sequence alignment software package

29 Jan 2015; Michał Górny (mgorny) fasta-35.4.10.ebuild,
fasta-36.3.5e.ebuild:
Convert to CPU_FLAGS_X86.
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

19 Apr 2015; Agostino Sarubbo (ago) fasttree-2.1.7.ebuild:
Stable for x86, wrt bug #544950
alphaamd64armhppaia64ppcppc64sparcx86
2.1.8 ~ ~
2.1.7 + +
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sci-biology/finchtv

Graphical viewer for chromatogram files

19 Apr 2015; Agostino Sarubbo (ago) finchtv-1.3.1-r2.ebuild:
Stable for x86, wrt bug #545798
alphaamd64armhppaia64ppcppc64sparcx86
1.3.1-r2 + +
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sci-biology/flower

Analyze 454 flowgrams (.SFF files)

19 Jan 2015; Sergei Trofimovich (slyfox)
+files/flower-0.7.2-ghc-7.8.patch, -flower-0.7-r1.ebuild, flower-0.7.2.ebuild:
Port to ghc-7.8 (bug #537052 by Toralf Förster).
alphaamd64armhppaia64ppcppc64sparcx86
0.7.2 ~ ~
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sci-biology/foldingathome

Folding@Home is a distributed computing project for protein folding

10 Aug 2014; Sergei Trofimovich (slyfox)
foldingathome-7.3.6-r2.ebuild, foldingathome-7.4.4.ebuild:
QA: drop trailing '.' from DESCRIPTION
alphaamd64armhppaia64ppcppc64sparcx86
7.4.4 ~ ~
7.3.6-r2 ~ ~
sci-biology Homepage FAH-EULA-2014 FAH-special-permission ChangeLog Metadata Similar Bugs Forums

sci-biology/gatk

The Genome Analysis Toolkit

*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 ~
sci-biology Homepage MIT ChangeLog Metadata Similar Bugs Forums

sci-biology/GBrowse

Generic Model Organism Database Project - The Generic Genome Browser

*GBrowse-2.48-r1 (27 Aug 2014)
27 Aug 2014; Ian Stakenvicius (_AxS_) (axs)
+GBrowse-2.48-r1.ebuild, -GBrowse-2.48.ebuild:
bumped EAPI to 5 to support dev-lang/perl upgrades
alphaamd64armhppaia64ppcppc64sparcx86
2.48-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 + +
sci-biology Homepage GPL-2 ChangeLog Metadata Similar Bugs Forums

sci-biology/glimmer

An HMM-based microbial gene finding system from TIGR

27 May 2015; Agostino Sarubbo (ago) glimmer-3.02-r3.ebuild:
Stable for x86, wrt bug #550436
alphaamd64armhppaia64ppcppc64sparcx86
3.02b ~ ~
3.02-r3 + +
sci-biology Homepage Artistic ChangeLog Metadata Similar Bugs Forums

sci-biology/glimmerhmm

A eukaryotic gene finding system from TIGR

17 Jan 2014; Jeroen Roovers (jer) glimmerhmm-3.0.1-r1.ebuild:
Spelling.
alphaamd64armhppaia64ppcppc64sparcx86
3.0.1-r1 + +
sci-biology Homepage Artistic ChangeLog Metadata Similar Bugs Forums

sci-biology/gmap

A Genomic Mapping and Alignment Program for mRNA and EST Sequences

11 Mar 2013; Justin Lecher (jlec) metadata.xml:
Drop Andrey as maintainer so that bugs get assigned to sci-biology directly
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

11 Mar 2013; Justin Lecher (jlec) metadata.xml:
Drop Andrey as maintainer so that bugs get assigned to sci-biology directly
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

alphaamd64armhppaia64ppcppc64sparcx86
2.0.1 ~ ~
1.9.8.1 ~ ~
1.9.7.3 ~ ~
sci-biology Homepage GPL-3 ChangeLog Metadata Similar Bugs Forums

sci-biology/hmmer

Sequence analysis using profile hidden Markov models

29 Jan 2015; Michał Górny (mgorny) hmmer-3.0.ebuild:
Switch to CPU_FLAGS_X86.
alphaamd64armhppaia64ppcppc64sparcx86
3.0 + +
2.3.2-r2 ~ + ~ ~ + ~ +
2.3.2-r1 ~ + + ~ ~ +
sci-biology Homepage GPL-3 ChangeLog Metadata Similar Bugs Forums

sci-biology/iedera

A subset seed design tool for DNA sequence alignment

11 Mar 2013; Justin Lecher (jlec) metadata.xml:
Drop Andrey as maintainer so that bugs get assigned to sci-biology directly
alphaamd64armhppaia64ppcppc64sparcx86
1.04 ~ ~
sci-biology Homepage GPL-2 ChangeLog Metadata Similar Bugs Forums

sci-biology/infernal

Inference of RNA alignments

06 Jul 2014; Justin Lecher (jlec) infernal-1.0.2-r1.ebuild,
+files/infernal-1.0.2-perl-5.16-2.patch,
-files/infernal-1.0.2-perl-5.16.patch:
Add patch as binary to prevent CVS magics, #431076
alphaamd64armhppaia64ppcppc64sparcx86
1.0.2-r1 + +
sci-biology Homepage GPL-3 ChangeLog Metadata Similar Bugs Forums

sci-biology/iqpnni

Important Quartet Puzzling and NNI Operation

11 Mar 2013; Justin Lecher (jlec) metadata.xml:
Drop Andrey as maintainer so that bugs get assigned to sci-biology directly
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

11 Mar 2013; Justin Lecher (jlec) metadata.xml:
Drop Andrey as maintainer so that bugs get assigned to sci-biology directly
alphaamd64armhppaia64ppcppc64sparcx86
2.03-r1 + +
2.03 + +
sci-biology Homepage GPL-2 ChangeLog Metadata Similar Bugs Forums

sci-biology/lagan

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

11 Mar 2013; Justin Lecher (jlec) metadata.xml:
Drop Andrey as maintainer so that bugs get assigned to sci-biology directly
alphaamd64armhppaia64ppcppc64sparcx86
2.0-r2 ~ ~
2.0-r1 ~ ~
sci-biology Homepage GPL-2 ChangeLog Metadata Similar Bugs Forums

sci-biology/last

Genome-scale comparison of biological sequences

08 Apr 2015; Michał Górny (mgorny) last-299.ebuild:
Drop old Python implementations
alphaamd64armhppaia64ppcppc64sparcx86
299 ~ ~
230 + +
sci-biology Homepage GPL-3 ChangeLog Metadata Similar Bugs Forums

sci-biology/mafft

Multiple sequence alignments using a variety of algorithms

19 Apr 2015; Agostino Sarubbo (ago) mafft-7.050.ebuild:
Stable for x86, wrt bug #544952
alphaamd64armhppaia64ppcppc64sparcx86
7.215 ~ ~
7.050 + +
sci-biology Homepage BSD ChangeLog Metadata Similar Bugs Forums

sci-biology/mammoth

MAtching Molecular Models Obtained from THeory

*mammoth-1.0-r1 (05 Mar 2015)
05 Mar 2015; Justin Lecher (jlec) +mammoth-1.0-r1.ebuild,
-mammoth-1.0.ebuild, metadata.xml:
EAPI Bump
alphaamd64armhppaia64ppcppc64sparcx86
1.0-r1 ~ ~
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

11 Mar 2013; Justin Lecher (jlec) metadata.xml:
Drop Andrey as maintainer so that bugs get assigned to sci-biology directly
alphaamd64armhppaia64ppcppc64sparcx86
0.7.1-r1 + +
0.7.1 + +
sci-biology Homepage GPL-3 ChangeLog Metadata Similar Bugs Forums

sci-biology/maqview

GUI for sci-biology/maq, a short read mapping assembler

11 Aug 2013; Justin Lecher (jlec) -maqview-0.2.5.ebuild,
-maqview-0.2.5-r1.ebuild:
Drop old
alphaamd64armhppaia64ppcppc64sparcx86
0.2.5-r2 + +
sci-biology Homepage GPL-3 ChangeLog Metadata Similar Bugs Forums

sci-biology/mauve

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

11 Mar 2013; Justin Lecher (jlec) metadata.xml:
Drop Andrey as maintainer so that bugs get assigned to sci-biology directly
alphaamd64armhppaia64ppcppc64sparcx86
9999
sci-biology Homepage GPL-2 ChangeLog Metadata Similar Bugs Forums

sci-biology/mauvealigner

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

11 Mar 2013; Justin Lecher (jlec) metadata.xml:
Drop Andrey as maintainer so that bugs get assigned to sci-biology directly
alphaamd64armhppaia64ppcppc64sparcx86
9999
sci-biology Homepage GPL-2 ChangeLog Metadata Similar Bugs Forums

sci-biology/mcl

A Markov Cluster Algorithm implementation

11 Mar 2013; Justin Lecher (jlec) metadata.xml:
Drop Andrey as maintainer so that bugs get assigned to sci-biology directly
alphaamd64armhppaia64ppcppc64sparcx86
12.135 ~ ~
08.312 ~ ~
sci-biology Homepage GPL-2 ChangeLog Metadata Similar Bugs Forums

sci-biology/meme

The MEME/MAST system - Motif discovery and search

19 Oct 2014; Patrick Lauer (patrick) meme-4.8.1-r2.ebuild:
Fix header
alphaamd64armhppaia64ppcppc64sparcx86
4.8.1-r2 + +
sci-biology Homepage meme ChangeLog Metadata Similar Bugs Forums

sci-biology/mira

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

25 Jan 2015; Justin Lecher (jlec) mira-4.0.2.ebuild,
+files/mira-4.0.2-cout.patch:
Build fix for newer gcc, #537564
alphaamd64armhppaia64ppcppc64sparcx86
4.0.2 ~ ~
3.9.18 + +
sci-biology Homepage GPL-2 ChangeLog Metadata Similar Bugs Forums

sci-biology/mosaik

A reference-guided aligner for next-generation sequencing technologies

11 Mar 2013; Justin Lecher (jlec) metadata.xml:
Drop Andrey as maintainer so that bugs get assigned to sci-biology directly
alphaamd64armhppaia64ppcppc64sparcx86
1.0.1388 ~ ~
1.0.1367 + +
sci-biology Homepage GPL-2 ChangeLog Metadata Similar Bugs Forums

sci-biology/mothur

A suite of algorithms for ecological bioinformatics

11 Mar 2013; Justin Lecher (jlec) metadata.xml:
Drop Andrey as maintainer so that bugs get assigned to sci-biology directly
alphaamd64armhppaia64ppcppc64sparcx86
1.27.0 ~ ~
1.13.0-r2 ~ ~
1.13.0-r1 ~ ~
1.6.0 + +
sci-biology Homepage GPL-3 ChangeLog Metadata Similar Bugs Forums

sci-biology/mrbayes

Bayesian Inference of Phylogeny

*mrbayes-3.1.2-r2 (17 Apr 2015)
17 Apr 2015; Justin Lecher (jlec) +mrbayes-3.1.2-r2.ebuild,
metadata.xml, mrbayes-3.1.2-r1.ebuild:
Import changes from science overlay
alphaamd64armhppaia64ppcppc64sparcx86
3.1.2-r2 ~ ~
3.1.2-r1 + +
sci-biology Homepage GPL-2 ChangeLog Metadata Similar Bugs Forums

sci-biology/mummer

A rapid whole genome aligner

11 Mar 2013; Justin Lecher (jlec) metadata.xml:
Drop Andrey as maintainer so that bugs get assigned to sci-biology directly
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

21 Apr 2015; Pacho Ramos (pacho) muscle-3.8.31.ebuild:
ppc stable wrt bug #544956
alphaamd64armhppaia64ppcppc64sparcx86
3.8.31 + + +
sci-biology Homepage public-domain ChangeLog Metadata Similar Bugs Forums

sci-biology/ncbi-tools

Development toolkit and applications for computational biology, including NCBI BLAST

11 Mar 2015; Justin Lecher (jlec) ncbi-tools-2.2.26-r2.ebuild:
Add missing X deps, #542558
alphaamd64armhppaia64ppcppc64sparcx86
2.2.26-r2 ~ + + +
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)

11 Mar 2013; Justin Lecher (jlec) metadata.xml:
Drop Andrey as maintainer so that bugs get assigned to sci-biology directly
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

*njplot-2.3-r1 (02 Mar 2015)
02 Mar 2015; Justin Lecher (jlec)
+files/njplot-2.3-buildsystem.patch, +files/njplot-2.3-format-security.patch,
+njplot-2.3-r1.ebuild, njplot-2.3.ebuild:
Fix dependencies, #425710; make buildsystem sane; fix format-security
alphaamd64armhppaia64ppcppc64sparcx86
2.3-r1 ~ ~
2.3 + +
sci-biology Homepage public-domain ChangeLog Metadata Similar Bugs Forums

sci-biology/pals

Pairwise Aligner for Long Sequences

11 Mar 2013; Justin Lecher (jlec) metadata.xml:
Drop Andrey as maintainer so that bugs get assigned to sci-biology directly
alphaamd64armhppaia64ppcppc64sparcx86
1.0 + +
sci-biology Homepage public-domain ChangeLog Metadata Similar Bugs Forums

sci-biology/paml

Phylogenetic Analysis by Maximum Likelihood

19 Apr 2015; Agostino Sarubbo (ago) paml-4.4c-r1.ebuild:
Stable for x86, wrt bug #544958
alphaamd64armhppaia64ppcppc64sparcx86
4.4c-r1 + +
sci-biology Homepage free-noncomm ChangeLog Metadata Similar Bugs Forums

sci-biology/phrap

Phrap, swat, cross_match: Shotgun assembly and alignment utilities

11 Mar 2013; Justin Lecher (jlec) metadata.xml:
Drop Andrey as maintainer so that bugs get assigned to sci-biology directly
alphaamd64armhppaia64ppcppc64sparcx86
1.080812 ~ ~
sci-biology Homepage phrap ChangeLog Metadata Similar Bugs Forums

sci-biology/phred

A base caller for Sanger DNA sequencing

11 Mar 2013; Justin Lecher (jlec) metadata.xml:
Drop Andrey as maintainer so that bugs get assigned to sci-biology directly
alphaamd64armhppaia64ppcppc64sparcx86
071220 ~ ~
sci-biology Homepage phrap ChangeLog Metadata Similar Bugs Forums

sci-biology/phylip

The PHYLogeny Inference Package

21 Apr 2015; Pacho Ramos (pacho) phylip-3.69-r1.ebuild:
ppc stable wrt bug #544946
alphaamd64armhppaia64ppcppc64sparcx86
3.696 ~ ~ ~
3.69-r1 + + +
sci-biology Homepage BSD-2 ChangeLog Metadata Similar Bugs Forums

sci-biology/phyml

Estimation of large phylogenies by maximum likelihood

14 Jan 2014; Agostino Sarubbo (ago) phyml-2.4.5-r2.ebuild:
Stable for ppc, wrt bug #497216
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

24 Nov 2013; Johann Schmitz (ercpe) -picard-1.58.ebuild,
-picard-1.63.ebuild:
Dropped versions 1.58 and 1.63 as they don't meet the qa requirements and a
snapshotted version of the lastest version is in the tree (#491816).
alphaamd64armhppaia64ppcppc64sparcx86
1.103 ~ ~
sci-biology Homepage Apache-2.0 ChangeLog Metadata Similar Bugs Forums

sci-biology/piler

Analysis of repetitive DNA found in genome sequences

11 Mar 2013; Justin Lecher (jlec) metadata.xml:
Drop Andrey as maintainer so that bugs get assigned to sci-biology directly
alphaamd64armhppaia64ppcppc64sparcx86
1.0 + +
sci-biology Homepage public-domain ChangeLog Metadata Similar Bugs Forums

sci-biology/pilercr

Analysis of Clustered Regularly Interspaced Short Palindromic Repeats (CRISPRs)

11 Mar 2013; Justin Lecher (jlec) metadata.xml:
Drop Andrey as maintainer so that bugs get assigned to sci-biology directly
alphaamd64armhppaia64ppcppc64sparcx86
1.0 + +
sci-biology Homepage public-domain ChangeLog Metadata Similar Bugs Forums

sci-biology/plink

Whole genome association analysis toolset

22 Sep 2014; Justin Lecher (jlec) plink-1.90_pre140514.ebuild:
Rename USE lapack -> blas, fixing build problems, #514106
alphaamd64armhppaia64ppcppc64sparcx86
1.90_pre140514 ~ ~
1.07-r1 + +
sci-biology Homepage GPL-2 ChangeLog Metadata Similar Bugs Forums

sci-biology/poa

Fast multiple sequence alignments using partial-order graphs

21 Mar 2015; Justin Lecher (jlec) -poa-2.ebuild, metadata.xml,
poa-2-r1.ebuild:
Drop old; BUmp EAPI; handle static-libs
alphaamd64armhppaia64ppcppc64sparcx86
2-r1 ~ ~
sci-biology Homepage GPL-2 ChangeLog Metadata Similar Bugs Forums

sci-biology/prank

Probabilistic Alignment Kit

*prank-140603 (29 Mar 2015)
29 Mar 2015; Justin Lecher (jlec) +prank-140603.ebuild,
prank-100701.ebuild, prank-111130.ebuild:
Version Bump
alphaamd64armhppaia64ppcppc64sparcx86
140603 ~ ~
111130 ~ ~
100701 ~ ~
sci-biology Homepage GPL-3 ChangeLog Metadata Similar Bugs Forums

sci-biology/primer3

Primer Design for PCR reactions

21 Apr 2015; Pacho Ramos (pacho) primer3-2.3.5.ebuild:
ppc stable wrt bug #544908
alphaamd64armhppaia64ppcppc64sparcx86
2.3.6 ~ ~ ~ ~ ~
2.3.5 + + ~ ~ +
sci-biology Homepage GPL-2 ChangeLog Metadata Similar Bugs Forums

sci-biology/prints

A protein motif fingerprint database

08 Mar 2012; Justin Lecher (jlec) -prints-38.0.ebuild:
Dropped old
alphaamd64armhppaia64ppcppc64sparcx86
39.0 + + +
sci-biology Homepage public-domain ChangeLog Metadata Similar Bugs Forums

sci-biology/probcons

Probabilistic Consistency-based Multiple Alignment of Amino Acid Sequences

alphaamd64armhppaia64ppcppc64sparcx86
1.12-r1 + +
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

*profphd-1.0.40 (24 Apr 2014)
24 Apr 2014; Justin Lecher (jlec) profphd-1.0.39.ebuild,
+profphd-1.0.40.ebuild, +files/profphd-1.0.39-perl.patch:
Fix for newer perl, version Bump
alphaamd64armhppaia64ppcppc64sparcx86
1.0.40 ~ ~
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

14 May 2014; Justin Lecher (jlec) psipred-3.1.ebuild,
psipred-3.2.ebuild, psipred-3.2.1.ebuild, psipred-3.3.ebuild,
psipred-3.4.ebuild, psipred-3.5.ebuild:
Add additional dep on sci-biology/update-blast
alphaamd64armhppaia64ppcppc64sparcx86
3.5 ~ ~
3.4 ~ ~
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

13 Apr 2015; Justin Lecher (jlec) pysam-0.6-r1.ebuild:
Keyword for x86
alphaamd64armhppaia64ppcppc64sparcx86
0.6-r1 ~ ~
sci-biology Homepages: 1 2 MIT ChangeLog Metadata Similar Bugs Forums

sci-biology/qrna

Prototype ncRNA genefinder

06 Dec 2012; Justin Lecher (jlec) -qrna-2.0.3c.ebuild:
Drop old
alphaamd64armhppaia64ppcppc64sparcx86
2.0.3c-r1 + ~ +
sci-biology Homepage GPL-2 ChangeLog Metadata Similar Bugs Forums

sci-biology/raxml

Sequential, Parallel & Distributed Inference of Large Phylogenetic Trees

29 Mar 2015; Justin Lecher (jlec) raxml-7.2.6.ebuild:
Use REQUIRED_USE to constrain sse3 compatibility
alphaamd64armhppaia64ppcppc64sparcx86
7.2.6 ~ ~
sci-biology Homepage GPL-2 ChangeLog Metadata Similar Bugs Forums

sci-biology/readseq

Reads and writes nucleic/protein sequences in various formats

10 Aug 2014; Sergei Trofimovich (slyfox)
readseq-20080420-r1.ebuild, readseq-20100513.ebuild:
QA: drop trailing '.' from DESCRIPTION
alphaamd64armhppaia64ppcppc64sparcx86
20100513 ~ ~
20080420-r1 ~ ~
sci-biology Homepage public-domain ChangeLog Metadata Similar Bugs Forums

sci-biology/rebase

A restriction enzyme database

*rebase-1506 (30 May 2015)
30 May 2015; Justin Lecher (jlec) +rebase-1506.ebuild:
Version Bump
alphaamd64armhppaia64ppcppc64sparcx86
1506 ~ ~ ~
1505 ~ ~ ~
1504 + + +
sci-biology Homepage public-domain ChangeLog Metadata Similar Bugs Forums

sci-biology/recon

Automated de novo identification of repeat families from genomic sequences

11 Mar 2013; Justin Lecher (jlec) metadata.xml:
Drop Andrey as maintainer so that bugs get assigned to sci-biology directly
alphaamd64armhppaia64ppcppc64sparcx86
1.06-r2 ~ ~
1.06-r1 ~ ~
sci-biology Homepages: 1 2 GPL-2 ChangeLog Metadata Similar Bugs Forums

sci-biology/repeatmasker

Screen DNA sequences for interspersed repeats and low complexity DNA

11 Mar 2013; Justin Lecher (jlec) metadata.xml:
Drop Andrey as maintainer so that bugs get assigned to sci-biology directly
alphaamd64armhppaia64ppcppc64sparcx86
4.0.1 ~ ~
sci-biology Homepage OSL-2.1 ChangeLog Metadata Similar Bugs Forums

sci-biology/repeatmasker-libraries

A special version of RepBase used by RepeatMasker

11 Mar 2013; Justin Lecher (jlec) metadata.xml:
Drop Andrey as maintainer so that bugs get assigned to sci-biology directly
alphaamd64armhppaia64ppcppc64sparcx86
20120418 ~ ~
sci-biology Homepage all-rights-reserved ChangeLog Metadata Similar Bugs Forums

sci-biology/rmblast

RepeatMasker compatible version of NCBI BLAST+

11 Mar 2013; Justin Lecher (jlec) metadata.xml:
Drop Andrey as maintainer so that bugs get assigned to sci-biology directly
alphaamd64armhppaia64ppcppc64sparcx86
1.2-r1 ~ ~
1.2 ~ ~
sci-biology Homepage OSL-2.1 ChangeLog Metadata Similar Bugs Forums

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 ~ +
sci-biology Homepage public-domain ChangeLog Metadata Similar Bugs Forums

sci-biology/samtools

Utilities for SAM (Sequence Alignment/Map), a format for large nucleotide sequence alignments

08 Apr 2015; Michał Górny (mgorny) samtools-0.1.19-r2.ebuild:
Drop old Python implementations
alphaamd64armhppaia64ppcppc64sparcx86
1.2 ~ ~
1.1 ~ ~
1.0-r1 ~ ~
1.0 ~ ~
0.1.19-r2 ~ ~
0.1.12 + +
sci-biology Homepage MIT ChangeLog Metadata Similar Bugs Forums

sci-biology/seaview

A graphical multiple sequence alignment editor

14 Jan 2014; Justin Lecher (jlec) -seaview-4.3.3.ebuild:
Drop old
alphaamd64armhppaia64ppcppc64sparcx86
4.3.5 + + +
sci-biology Homepage public-domain ChangeLog Metadata Similar Bugs Forums

sci-biology/seqan

C++ Sequence Analysis Library

08 Apr 2015; Michał Górny (mgorny) seqan-1.3.1-r1.ebuild:
Drop old Python implementations
alphaamd64armhppaia64ppcppc64sparcx86
2.0.0 ~ ~
1.4.2 ~ ~
1.3.1-r1 ~ ~
sci-biology Homepage BSD GPL-3 ChangeLog Metadata Similar Bugs Forums

sci-biology/shrimp

SHort Read Mapping Package

08 Apr 2015; Michał Górny (mgorny) shrimp-2.2.3.ebuild:
Drop old Python implementations
alphaamd64armhppaia64ppcppc64sparcx86
2.2.3 ~ ~
2.0.1 + +
sci-biology Homepage shrimp ChangeLog Metadata Similar Bugs Forums

sci-biology/sibsim4

A rewrite and improvement upon sim4, a DNA-mRNA aligner

18 Jun 2013; Justin Lecher (jlec) metadata.xml:
Drop maintainer
alphaamd64armhppaia64ppcppc64sparcx86
0.20 + +
sci-biology Homepage GPL-2 ChangeLog Metadata Similar Bugs Forums

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

12 Mar 2013; Justin Lecher (jlec) metadata.xml:
Drop Andrey as maintainer so that bugs get assigned to sci-biology directly
alphaamd64armhppaia64ppcppc64sparcx86
2.0.1-r1 + +
2.0.1 + +
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sci-biology/stride

Protein secondary structure assignment from atomic coordinates

19 Apr 2015; Pacho Ramos (pacho) stride-20011129-r1.ebuild:
x86 stable wrt bug #525378
alphaamd64armhppaia64ppcppc64sparcx86
20011129-r1 + + +
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sci-biology/t-coffee

A multiple sequence alignment package

26 Apr 2015; Pacho Ramos (pacho) t-coffee-9.03.1318-r1.ebuild:
ppc stable wrt bug #544930
alphaamd64armhppaia64ppcppc64sparcx86
11.00 ~ ~ ~ ~
9.03.1318-r1 + + ~ +
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sci-biology/tophat

A fast splice junction mapper for RNA-Seq reads

17 Oct 2014; Sergey Popov (pinkbyte) tophat-1.0.12.ebuild:
Non-maintainer commit: fix building, approved by Justin Lecher
alphaamd64armhppaia64ppcppc64sparcx86
2.0.9 ~ ~
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

26 Oct 2010; Ryan Hill (dirtyepic) -treeviewx-0.5.1.ebuild,
-treeviewx-0.5.1-r1.ebuild:
Remove old.
alphaamd64armhppaia64ppcppc64sparcx86
0.5.1-r2 + +
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sci-biology/trf

Tandem Repeats Finder

17 Apr 2014; Ulrich Müller (ulm) trf-4.04.ebuild:
Fix LICENSE, add mirror and bindist restrictions, update SRC_URI, bug 470778.
alphaamd64armhppaia64ppcppc64sparcx86
4.04 + +
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sci-biology/trnascan-se

tRNA detection in large-scale genome sequences

*trnascan-se-1.31 (08 Jan 2015)
08 Jan 2015; Justin Lecher (jlec) -trnascan-se-1.23-r1.ebuild,
+trnascan-se-1.31.ebuild, +files/trnascan-se-1.31-ldflags.patch,
metadata.xml:
Version BUmp, #532460
alphaamd64armhppaia64ppcppc64sparcx86
1.31 ~ ~
1.23-r2 + +
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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

17 Apr 2015; Justin Lecher (jlec) -ucsc-genome-browser-223.ebuild,
ucsc-genome-browser-260.ebuild:
Drop old; bump EAPI
alphaamd64armhppaia64ppcppc64sparcx86
260 ~ ~
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sci-biology/unafold

Unified Nucleic Acid Folding and hybridization package

12 Mar 2013; Justin Lecher (jlec) metadata.xml:
Drop Andrey as maintainer so that bugs get assigned to sci-biology directly
alphaamd64armhppaia64ppcppc64sparcx86
3.8-r1 ~ ~
3.8 ~ ~
sci-biology Homepage unafold ChangeLog Metadata Similar Bugs Forums

sci-biology/update-blastdb

update_blastdb.pl for local blast db maintainance

19 May 2014; Justin Lecher (jlec) update-blastdb-12.0.0.ebuild:
Fix typo
alphaamd64armhppaia64ppcppc64sparcx86
12.0.0 ~ ~
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sci-biology/vaal

A variant ascertainment algorithm that can be used to detect SNPs, indels, and other polymorphisms

24 Mar 2015; Agostino Sarubbo (ago) vaal-46233.ebuild:
Stable for amd64, wrt bug #543404
alphaamd64armhppaia64ppcppc64sparcx86
46233 +
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sci-biology/vcftools

Tools for working with VCF (Variant Call Format) files

*vcftools-0.1.12b (03 Apr 2015)
03 Apr 2015; Andreas K. Huettel (dilfridge)
+vcftools-0.1.12b.ebuild, +files/vcftools-0.1.12b-buildsystem.patch:
Version bump, fixing bug 545304
alphaamd64armhppaia64ppcppc64sparcx86
0.1.12b ~ ~
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sci-biology/velvet

A sequence assembler for very short reads

*velvet-1.2.10 (28 Dec 2013)
28 Dec 2013; Justin Lecher (jlec) +velvet-1.2.10.ebuild:
Import Version BUmp from sci overlay, thanks mahn for the ebuild, #495094
alphaamd64armhppaia64ppcppc64sparcx86
1.2.10 ~ ~
1.0.18-r1 + +
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sci-biology/vienna-rna

RNA secondary structure prediction and comparison

16 Nov 2014; Andreas K. Huettel (dilfridge)
vienna-rna-2.1.1.ebuild, vienna-rna-2.1.8.ebuild:
Replace fixlocalpod with perl_delete_localpod
alphaamd64armhppaia64ppcppc64sparcx86
2.1.8 ~ ~ ~
2.1.1 + + +
sci-biology Homepage vienna-rna ChangeLog Metadata Similar Bugs Forums

sci-biology/wgs-assembler

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

12 Mar 2013; Justin Lecher (jlec) metadata.xml:
Drop Andrey as maintainer so that bugs get assigned to sci-biology directly
alphaamd64armhppaia64ppcppc64sparcx86
7.0-r1 + +
7.0 ~ ~
6.1 ~ +
5.4 + +
sci-biology Homepage GPL-2 ChangeLog Metadata Similar Bugs Forums

sci-biology/wise

Intelligent algorithms for DNA searches

19 Apr 2015; Agostino Sarubbo (ago) wise-2.4.0_alpha.ebuild:
Stable for x86, wrt bug #544940
alphaamd64armhppaia64ppcppc64sparcx86
2.4.0_alpha ~ + + ~ +
sci-biology Homepage BSD ChangeLog Metadata Similar Bugs Forums

sci-biology/yass

Genomic similarity search with multiple transition constrained spaced seeds

12 Mar 2013; Justin Lecher (jlec) metadata.xml:
Drop Andrey as maintainer so that bugs get assigned to sci-biology directly
alphaamd64armhppaia64ppcppc64sparcx86
1.14-r1 ~ ~
1.14 ~ ~
sci-biology Homepage GPL-2 ChangeLog Metadata Similar Bugs Forums

Last update:
03 Jun 2015
19:01 UTC

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