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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

13 Nov 2013; Patrick Lauer (patrick) allpathslg-42337.ebuild,
allpathslg-47093.ebuild:
Removing x86 keyword as dependency sci-biology/vaal does not work on x86
alphaamd64armhppaia64ppcppc64sparcx86
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

*amos-3.1.0-r1 (29 Dec 2013)
29 Dec 2013; Justin Lecher (jlec) +amos-3.1.0-r1.ebuild,
+files/amos-3.1.0-goBambus2.py-indent-and-cleanup.patch:
Fix python support
alphaamd64armhppaia64ppcppc64sparcx86
3.1.0-r1 ~ ~
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

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 ~ ~
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sci-biology/bioperl

Perl tools for bioinformatics - Core modules

09 Aug 2014; Mikle Kolyada (zlogene) bioperl-1.6.0-r2.ebuild,
bioperl-1.6.9.ebuild, bioperl-9999-r1.ebuild:
Bump to EAPI=5 (bug #478714)
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

09 Aug 2014; Mikle Kolyada (zlogene) bioperl-db-1.6.0.ebuild,
bioperl-db-1.6.9.ebuild, bioperl-db-9999-r1.ebuild:
Bump to EAPI=5 (bug #478714)
alphaamd64armhppaia64ppcppc64sparcx86
9999-r1
1.6.9 ~ ~
1.6.0 + +
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

alphaamd64armhppaia64ppcppc64sparcx86
9999-r1
1.6.9 ~ ~
1.6.0 + +
sci-biology Homepage Artistic GPL-2 ChangeLog Metadata Similar Bugs Forums

sci-biology/bioperl-run

Perl tools for bioinformatics - Wrapper modules around key bioinformatics applications

alphaamd64armhppaia64ppcppc64sparcx86
9999-r1
1.6.9 ~ ~
1.6.1 + +
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sci-biology/biopython

Python modules for computational molecular biology

*biopython-1.64 (03 Jun 2014)
03 Jun 2014; Justin Lecher (jlec) +biopython-1.64.ebuild:
Version Bump, thanks Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> preparing
the ebuild
alphaamd64armhppaia64ppcppc64sparcx86
1.64 ~ ~ ~
1.63-r1 ~ ~ ~
1.63 ~ ~ ~
1.62-r1 ~ ~ ~
1.62 ~ ~ ~
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

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 + +
sci-biology Homepage Artistic ChangeLog Metadata Similar Bugs Forums

sci-biology/bwa

Burrows-Wheeler Alignment Tool, a fast short 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
0.6.2 ~ ~
0.6.1 ~ ~
0.5.9 ~ ~
0.5.0-r1 ~ ~
0.5.0 + +
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 ~ ~
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sci-biology/clustal-omega

Scalable multiple alignment of protein sequences

*clustal-omega-1.2.0 (06 Jan 2014)
06 Jan 2014; Justin Lecher (jlec) +clustal-omega-1.2.0.ebuild:
Version Bump
alphaamd64armhppaia64ppcppc64sparcx86
1.2.0 ~ ~
1.1.0 ~ ~
1.0.3 ~ ~
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

*clustalx-2.1-r1 (06 Jan 2014)
06 Jan 2014; Justin Lecher (jlec) +clustalx-2.1-r1.ebuild:
Make sure only system libs are used
alphaamd64armhppaia64ppcppc64sparcx86
2.1-r1 ~ ~
2.1 + +
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sci-biology/consed

A genome sequence finishing program

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

sci-biology/cufflinks

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

*cufflinks-1.3.0-r1 (05 Feb 2014)
05 Feb 2014; Sergey Popov (pinkbyte) -cufflinks-1.3.0.ebuild,
+cufflinks-1.3.0-r1.ebuild, files/cufflinks-1.3.0-autotools.patch:
Revision bump: EAPI 5, add subslot to Boost dependency, fix compatibility
with Automake 1.14, wrt bug #499046. Drop old revision
alphaamd64armhppaia64ppcppc64sparcx86
1.3.0-r1 ~ ~
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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

11 Mar 2013; Justin Lecher (jlec) metadata.xml:
Drop Andrey as maintainer so that bugs get assigned to sci-biology directly
alphaamd64armhppaia64ppcppc64sparcx86
1.0.2-r1 ~ ~
1.0.2 + +
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 ~ ~
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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 +
sci-biology Homepage Artistic ChangeLog Metadata Similar Bugs Forums

sci-biology/embassy

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

05 Apr 2011; Justin Lecher (jlec) -embassy-4.0.0.ebuild:
Dropped old, due to unsatisfied deps
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 + ~ +
sci-biology Homepage LGPL-2 GPL-2 ChangeLog Metadata Similar Bugs Forums

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

30 Jul 2014; Brian Evans (grknight) emboss-6.0.1.ebuild,
emboss-6.1.0-r1.ebuild, emboss-6.3.1_p4-r1.ebuild, emboss-6.3.1_p4.ebuild:
Non-maintainer commit. Update to use virtual/mysql wrt bug 508802
alphaamd64armhppaia64ppcppc64sparcx86
6.3.1_p4-r1 ~ ~ ~
6.3.1_p4 ~ ~ ~
6.1.0-r1 ~ ~ ~
6.0.1 + + +
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sci-biology/eugene

Eukaryotic gene predictor

*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 ~ ~
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sci-biology/express

Streaming RNA-Seq Analysis

*express-0.9.5-r1 (05 Feb 2014)
05 Feb 2014; Sergey Popov (pinkbyte) +express-0.9.5-r1.ebuild:
Revision bump: EAPI 5, add subslot to Boost dependency, fix underlinking on
Boost components, wrt bug #499038
alphaamd64armhppaia64ppcppc64sparcx86
0.9.5-r1 ~ ~
0.9.5 ~ ~
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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

*fasttree-2.1.7 (20 Dec 2013)
20 Dec 2013; Justin Lecher (jlec) +fasttree-2.1.7.ebuild,
+files/CMakeLists.txt, metadata.xml:
Version BUmp, #494662
alphaamd64armhppaia64ppcppc64sparcx86
2.1.7 ~ ~
2.0.1 ~ ~
sci-biology Homepage GPL-2 ChangeLog Metadata Similar Bugs Forums

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 + +
sci-biology Homepage finchtv ChangeLog Metadata Similar Bugs Forums

sci-biology/flower

Analyze 454 flowgrams (.SFF files)

*flower-0.7.2 (22 Sep 2013)
22 Sep 2013; Heather Cynede (cynede) +flower-0.7.2.ebuild:
flower version bump
alphaamd64armhppaia64ppcppc64sparcx86
0.7.2 ~ ~
0.7-r1 ~ ~
sci-biology Homepage GPL-2 ChangeLog Metadata Similar Bugs Forums

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

sci-biology/glimmer

An HMM-based microbial gene finding system from TIGR

11 Mar 2013; Justin Lecher (jlec) metadata.xml:
Drop Andrey as maintainer so that bugs get assigned to sci-biology directly
alphaamd64armhppaia64ppcppc64sparcx86
3.02-r2 + +
3.02-r1 + +
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 + +
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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

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

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 ~ + + ~ ~ +
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

11 Aug 2013; Justin Lecher (jlec) -last-146.ebuild,
-last-162-r1.ebuild, -last-184.ebuild, -last-192.ebuild:
Drop old
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 Jul 2013; Justin Lecher (jlec) mafft-7.050.ebuild:
Keyword for ~-linux
alphaamd64armhppaia64ppcppc64sparcx86
7.050 ~ ~
sci-biology Homepage BSD ChangeLog Metadata Similar Bugs Forums

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

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 Mar 2013; Justin Lecher (jlec) meme-4.8.1-r2.ebuild:
Fix renaming procedure, #460372
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

14 Jan 2014; Justin Lecher (jlec) -mira-3.2.1.ebuild:
Drop old
alphaamd64armhppaia64ppcppc64sparcx86
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

21 Dec 2011; Justin Lecher (jlec) -mrbayes-3.1.2.ebuild:
Cleaned old
alphaamd64armhppaia64ppcppc64sparcx86
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

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

sci-biology/ncbi-tools

Development toolkit and applications for computational biology, including NCBI BLAST

12 Jun 2013; Justin Lecher (jlec) ncbi-tools-2.2.26-r2.ebuild,
files/ncbirc:
Fix for prefix
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

11 Mar 2013; Justin Lecher (jlec) metadata.xml:
Drop Andrey as maintainer so that bugs get assigned to sci-biology directly
alphaamd64armhppaia64ppcppc64sparcx86
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

12 Sep 2010; Kacper Kowalik (xarthisius) -paml-4.3a.ebuild,
-paml-4.3b.ebuild:
Drop old buggy versions.
alphaamd64armhppaia64ppcppc64sparcx86
4.4c + +
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

PHYLIP - The PHYLogeny Inference Package

11 Mar 2013; Justin Lecher (jlec) metadata.xml:
Drop Andrey as maintainer so that bugs get assigned to sci-biology directly
alphaamd64armhppaia64ppcppc64sparcx86
3.69-r1 ~ ~ ~
3.69 + ~ +
3.67 + + +
sci-biology Homepage freedist 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

*plink-1.90_pre140514 (19 May 2014)
19 May 2014; Justin Lecher (jlec) -plink-1.07.ebuild,
+plink-1.90_pre140514.ebuild:
Version BUmp, #510716
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

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

sci-biology/prank

Probabilistic Alignment Kit

11 Mar 2013; Justin Lecher (jlec) metadata.xml:
Drop Andrey as maintainer so that bugs get assigned to sci-biology directly
alphaamd64armhppaia64ppcppc64sparcx86
111130 ~ ~
100701 ~ ~
sci-biology Homepages: 1 2 GPL-3 ChangeLog Metadata Similar Bugs Forums

sci-biology/primer3

Primer Design for PCR reactions

*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 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

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

*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

*pysam-0.6-r1 (30 Jun 2014)
30 Jun 2014; Mike Gilbert (floppym) +pysam-0.6-r1.ebuild,
-pysam-0.6.ebuild:
Convert to distutils-r1. Depend on setuptools.
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

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

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

15 Sep 2014; Justin Lecher (jlec) -rebase-1111.ebuild:
Drop ebuild with deprecated EAPI
alphaamd64armhppaia64ppcppc64sparcx86
1409 ~ ~ ~
1408 ~ ~ ~
1406 ~ ~ ~
1403 + + +
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 ~ +
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sci-biology/samtools

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

*samtools-1.0 (20 Sep 2014)
20 Sep 2014; Justin Lecher (jlec) -samtools-0.1.18.ebuild,
-samtools-0.1.18-r2.ebuild, -samtools-0.1.18-r3.ebuild,
samtools-0.1.19-r2.ebuild, +samtools-1.0.ebuild:
Version Bump, #523224; drop old
alphaamd64armhppaia64ppcppc64sparcx86
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 + + +
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sci-biology/seqan

C++ Sequence Analysis Library

17 Jul 2013; Justin Lecher (jlec) seqan-1.3.1-r1.ebuild:
Add missing dep
alphaamd64armhppaia64ppcppc64sparcx86
1.3.1-r1 ~ ~
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sci-biology/shrimp

SHort Read Mapping Package

05 Sep 2013; Michał Górny (mgorny) shrimp-2.2.3.ebuild:
Clean up PYTHON_COMPAT from old 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 + +
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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

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 + +
sci-biology Homepage GPL-3 ChangeLog Metadata Similar Bugs Forums

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

A multiple sequence alignment package

12 Mar 2013; Justin Lecher (jlec) metadata.xml:
Drop Andrey as maintainer so that bugs get assigned to sci-biology directly
alphaamd64armhppaia64ppcppc64sparcx86
9.03.1318-r1 ~ ~ ~
8.93 ~ ~ ~
8.69 + + +
sci-biology Homepage GPL-2 ChangeLog Metadata Similar Bugs Forums

sci-biology/tophat

A fast splice junction mapper for RNA-Seq reads

*tophat-2.0.9 (06 Mar 2014)
06 Mar 2014; Justin Lecher (jlec) +tophat-2.0.9.ebuild,
+files/tophat-2.0.9-flags.patch:
Version Bump, #502532; thanks José María Fernández González for the new
ebuild
alphaamd64armhppaia64ppcppc64sparcx86
2.0.9 ~ ~
2.0.8 ~ ~
2.0.2 ~ ~
2.0.0 ~ ~
1.4.1 ~ ~
1.0.12 + +
sci-biology Homepage Artistic ChangeLog Metadata Similar Bugs Forums

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

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

12 Mar 2013; Justin Lecher (jlec) metadata.xml:
Drop Andrey as maintainer so that bugs get assigned to sci-biology directly
alphaamd64armhppaia64ppcppc64sparcx86
260 ~ ~
223 ~ ~
sci-biology Homepage blat ChangeLog Metadata Similar Bugs Forums

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

12 Nov 2013; Justin Lecher (jlec) vaal-1.6.ebuild,
vaal-42179.ebuild, vaal-45166.ebuild, vaal-46233.ebuild:
Drop x86 as upstream gives no support and types are not easily fixable,
#458488, #472088 & #488550
alphaamd64armhppaia64ppcppc64sparcx86
46233 ~
45166 ~
42179 ~
1.6 +
sci-biology Homepage Whitehead-MIT ChangeLog Metadata Similar Bugs Forums

sci-biology/vcftools

Tools for working with VCF (Variant Call Format) files

12 Mar 2013; Justin Lecher (jlec) metadata.xml:
Drop Andrey as maintainer so that bugs get assigned to sci-biology directly
alphaamd64armhppaia64ppcppc64sparcx86
0.1.8 ~ ~
0.1.7 ~ ~
sci-biology Homepage GPL-3 ChangeLog Metadata Similar Bugs Forums

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

*vienna-rna-2.1.8 (15 Sep 2014)
15 Sep 2014; Justin Lecher (jlec) +vienna-rna-2.1.8.ebuild,
+files/vienna-rna-2.1.8-bindir.patch:
Version Bump, #522850
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

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

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:
21 Sep 2014
15:25 UTC

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