Pakiety oprogramowania w gałęzi "jessie-backports", Podsekcja science

abyss (2.0.2-1~bpo8+1)
de novo, parallel, sequence assembler for short reads
adapterremoval (2.2.0-1~bpo8+1)
rapid adapter trimming, identification, and read merging of gene sequences
adapterremoval-examples (2.2.0-1~bpo8+1)
rapid adapter trimming, identification, and read merging (example data)
altree (1.3.1-4~bpo8+1)
Program do wykonywania analiz dotyczących związku i miejsca na podstawie filogenezy
altree-examples (1.3.1-4~bpo8+1)
Przykładowe pliki do ALTree
ampliconnoise (1.29-6~bpo8+1)
removal of noise from 454 sequenced PCR amplicons
art-nextgen-simulation-tools (20160605+dfsg-1~bpo8+1)
simulation tools to generate synthetic next-generation sequencing reads
art-nextgen-simulation-tools-profiles (20160605+dfsg-1~bpo8+1)
profiles for art simulation tools
artemis (16.0.0+dfsg-4~bpo8+1)
genome browser and annotation tool
artfastqgenerator (0.0.20150519-1~bpo8+1)
ouputs artificial FASTQ files derived from a reference genome
artfastqgenerator-examples (0.0.20150519-1~bpo8+1)
ouputs artificial FASTQ files derived from a reference genome (examples)
astropy-utils (1.3-8~bpo8+2)
Command line tools from astropy
atac (0~20150903+r2013-3~bpo8+1)
genome assembly-to-assembly comparison
ballview (1.4.3~beta1-3~bpo8+1)
free molecular modeling and molecular graphics tool
barrnap (0.7+dfsg-1~bpo8+1)
rapid ribosomal RNA prediction
bcftools (1.3.1-1~bpo8+2)
genomic variant calling and manipulation of VCF/BCF files
beast-mcmc (1.8.4+dfsg.1-1~bpo8+1)
Bayesian MCMC phylogenetic inference
blasr (5.3+0-1~bpo8+1 [amd64, arm64, kfreebsd-amd64, ppc64el], 0~20151014+git8e668be-1~bpo8+1 [armel, i386, mipsel], 0~20150724+git3ca7fe8-1~bpo8+1 [armhf, mips, powerpc, s390x])
mapping single-molecule sequencing reads
boinc-app-seti (8.00~svn3363-3~bpo8+1)
SETI@home application for the BOINC client
boinc-app-seti-graphics (8.00~svn3363-3~bpo8+1)
SETI@home application for the BOINC client (with graphics)
bowtie2 (2.3.0-2~bpo8+1)
ultrafast memory-efficient short read aligner
bowtie2-examples (2.3.0-2~bpo8+1)
Examples for bowtie2
brig (0.95+dfsg-1~bpo8+1)
BLAST Ring Image Generator
bwa (0.7.15-2~bpo8+1)
Burrows-Wheeler Aligner
cbmc (5.2-1~bpo8+1)
bounded model checker for C and C++ programs
cgview (0.0.20100111-1~bpo8+1)
Circular Genome Viewer
chemps2 (1.6-1~bpo80+1)
Executable to call libchemps2-1 from the command line
circlator (1.4.0-1~bpo8+1)
circularize genome assemblies
clonalframe (1.2-5~bpo8+1)
inference of bacterial microevolution using multilocus sequence data
cp2k (2.6.1-2~bpo80+1)
Ab Initio Molecular Dynamics
cp2k-data (2.6.1-2~bpo80+1)
Ab Initio Molecular Dynamics (data files)
cutadapt (1.12-2~bpo8+1)
Clean biological sequences from high-throughput sequencing reads
cwltool (1.0.20170114120503-1~bpo8+1)
Common workflow language reference implementation
daligner (1.0+20160927-1~bpo8+1)
local alignment discovery between long nucleotide sequencing reads
dascrubber (0~20160601-1~bpo8+1)
alignment-based scrubbing pipeline for DNA sequencing reads
dazzdb (1.0+20160930-1~bpo8+1)
manage nucleotide sequencing read data
dh-r (20161219~bpo8+1)
Debian helper tools for packaging R libraries
ea-utils (1.1.2+dfsg-4~bpo8+1)
command-line tools for processing biological sequencing data
eigensoft (6.1.4+dfsg-1~bpo8+1)
reduction of population bias for genetic analyses
falcon (1.8.4-1~bpo8+1)
diploid-aware genome assembly of single-molecule sequencing reads
fastahack (0.0+20160702-1~bpo8+1)
utility for indexing and sequence extraction from FASTA files
fastaq (3.14.0-1~bpo8+1)
FASTA and FASTQ file manipulation tools
fastml (3.1-2~bpo8+1)
maximum likelihood ancestral amino-acid sequence reconstruction
fastqc (0.11.5+dfsg-6~bpo8+1)
quality control for high throughput sequence data
figtree (1.4.2+dfsg-2~bpo8+1)
graphical phylogenetic tree viewer
freecad (0.16+dfsg2-1~bpo8+1)
Rozszerzalny, otwartoźródłowy program CAx (alfa)
fsm-lite (1.0-2~bpo8+1)
frequency-based string mining (lite)
genometools (1.5.9+ds-2~bpo8+1)
versatile genome analysis toolkit
genometools-common (1.5.9+ds-2~bpo8+1)
shared data files for GenomeTools
ghkl (5.0.0.2173-2~bpo8+1)
diffractometer computation control application
gmt (5.3.1+dfsg-1~bpo8+1)
Generic Mapping Tools
gmt-common (5.3.1+dfsg-1~bpo8+1)
Generic Mapping Tools - Architecture-independent files
gmt-dcw (1.1.2-1~bpo8+1)
Digital Chart of the World (DCW) for GMT
gmt-gshhg (2.3.6-1~bpo8+1)
Global Self-consistent Hierarchical High-resolution Geography (GSHHG)
gmt-gshhg-full (2.3.6-1~bpo8+1)
Full resolution coastlines for the Generic Mapping Tools
gmt-gshhg-high (2.3.6-1~bpo8+1)
High resolution coastlines for the Generic Mapping Tools
gmt-gshhg-low (2.3.6-1~bpo8+1)
Low resolution coastlines for the Generic Mapping Tools
gr-fcdproplus (3.7.25.4b6464b-2~bpo8+2)
Funcube Dongle Pro Plus controller for GNU Radio
graphlan (1.1-1~bpo8+1)
circular representations of taxonomic and phylogenetic trees
gubbins (2.2.0-1~bpo8+1 [amd64], 1.4.4-1~bpo8+1 [i386])
phylogenetic analysis of genome sequences
gyoto (1.0.1-3~bpo8+1)
General relativistic ray-tracing
harvest-tools (1.3-1~bpo8+1 [amd64, arm64, i386, mips, mipsel, powerpc, ppc64el, s390x], 1.2-2~bpo8+1 [kfreebsd-amd64, kfreebsd-i386])
archiving and postprocessing for reference-compressed genomic multi-alignments
hilive (0.3-2~bpo8+1 [amd64, arm64, armel, i386, kfreebsd-amd64, kfreebsd-i386, mipsel, ppc64el], 0.0+20150926-1~bpo8+1 [s390x])
realtime alignment of Illumina reads
htslib-test (1.3.2-2~bpo8+1)
Test data for HTSlib
hyphy-common (2.2.7+dfsg-1~bpo8+1)
Hypothesis testing using Phylogenies (common files)
hyphy-mpi (2.2.7+dfsg-1~bpo8+1)
Hypothesis testing using Phylogenies (MPI version)
hyphy-pt (2.2.7+dfsg-1~bpo8+1)
Hypothesis testing using Phylogenies (pthreads version)
hyphygui (2.2.7+dfsg-1~bpo8+1)
Hypothesis testing using Phylogenies (GTK+ gui)
iqtree (1.5.3+dfsg-2~bpo8+1)
efficient phylogenetic software by maximum likelihood
jaligner (1.0+dfsg-4~bpo8+1)
Smith-Waterman algorithm with Gotoh's improvement
jellyfish (2.2.6-1~bpo8+1)
count k-mers in DNA sequences
jellyfish-examples (2.2.6-1~bpo8+1)
count k-mers in DNA sequences (examples for testing)
jmodeltest (2.1.10+dfsg-2~bpo8+1)
HPC selection of models of nucleotide substitution
jmol (14.6.4+2016.11.05+dfsg1-3~bpo8+1)
Molecular Viewer
josm-plugins (0.0.svn33112+ds-1~bpo8+1)
Plugins for JOSM
jupyter-notebook (4.2.3-4~bpo8+1)
Jupyter interactive notebook
kineticstools (0.5.1+20150828+git3aa3d96+dfsg-1~bpo8+1)
detection of DNA modifications
kmer (0~20150903+r2013-3~bpo8+1)
suite of tools for DNA sequence analysis
kraken (0.10.5~beta-1~bpo8+1)
assigning taxonomic labels to short DNA sequences
lammps (0~20161109.git9806da6-7~bpo8+1)
Molecular Dynamics Simulator
last-align (830-1~bpo8+1)
Porównywanie sekwencji biologicznych w skali genomu
leaff (0~20150903+r2013-3~bpo8+1)
biological sequence library utilities and applications
lefse (1.0+20160802-1~bpo8+1)
determine features of organisms, clades, taxonomic units, genes
libball1.4-data (1.4.3~beta1-3~bpo8+1)
Biochemical Algorithms Library (data files)
libgnuradio-fcdproplus3.7.10 (3.7.25.4b6464b-2~bpo8+2)
Funcube Dongle Pro Plus controller for GNU Radio (runtime)
libgyoto4 (1.0.1-3~bpo8+1)
General relativistic geodesic integration and ray-tracing
libliggghts3 (3.5.0+repack1-10~bpo8+1 [amd64, arm64, armel, armhf, i386, powerpc, ppc64el, s390x], 3.3.1+repack1-1~bpo8+1 [mips, mipsel])
Open Source DEM Particle Simulation Software. Shared library
libncarg-bin (6.3.0-4~bpo8+1)
NCAR command-language library - development tools
libncarg-data (6.3.0-4~bpo8+1)
NCAR command-language library - Data
libopenfoam (4.0+dfsg1-7~bpo8+1)
Set of programs for Computational Fluid Dynamics (CFD). Libraries
libqgis-customwidgets (2.14.11+dfsg-1~bpo8+1)
QGIS custom widgets for Qt Designer
libqgis-server2.14.11 (2.14.11+dfsg-1~bpo8+1)
QGIS - shared server library
libvcflib-tools (1.0.0~rc1+dfsg1-3~bpo8+1)
C++ library for parsing and manipulating VCF files (tools)
libyade (2017.01a-7~bpo8+1 [amd64, arm64, i386, kfreebsd-amd64, powerpc, ppc64el, s390x], 1.20.0-2~bpo8+1 [armel, armhf, mips, mipsel])
Platform for discrete element modeling. Libraries
liggghts (3.5.0+repack1-10~bpo8+1 [amd64, arm64, armel, armhf, i386, powerpc, ppc64el, s390x], 3.3.1+repack1-1~bpo8+1 [mips, mipsel])
Open Source DEM Particle Simulation Software.
maffilter (1.1.0-1+dfsg-2~bpo8+1)
process genome alignment in the Multiple Alignment Format
maffilter-examples (1.1.0-1+dfsg-2~bpo8+1)
process genome alignment in the Multiple Alignment Format (example data)
mapdamage (2.0.6+dfsg-1~bpo8+1)
tracking and quantifying damage patterns in ancient DNA sequences
mauve-aligner (2.4.0+4734-3~bpo8+1)
multiple genome alignment
meryl (0~20150903+r2013-3~bpo8+1)
in- and out-of-core kmer counting and utilities
metaphlan2 (2.6.0+ds-1~bpo8+1)
Metagenomic Phylogenetic Analysis
metaphlan2-data (2.6.0+ds-2~bpo8+1)
data package for Metagenomic Phylogenetic Analysis
mhap (2.1.1+dfsg-1~bpo8+1)
locality-sensitive hashing to detect long-read overlaps
microbegps (1.0.0-2~bpo8+1)
explorative taxonomic profiling tool for metagenomic data
murasaki (1.68.6-5~bpo8+1)
homology detection tool across multiple large genomes
murasaki-common (1.68.6-5~bpo8+1)
homology detection tool across multiple large genomes (common files)
murasaki-mpi (1.68.6-5~bpo8+1)
homology detection tool across multiple large genomes (MPI-version)
nanopolish (0.5.0-1~bpo8+1)
consensus caller for nanopore sequencing data
ncbi-blast+ (2.6.0-1~bpo8+1)
next generation suite of BLAST sequence search tools
ncbi-blast+-legacy (2.6.0-1~bpo8+1)
NCBI Blast legacy call script
ncbi-rrna-data (6.1.20170106-2~bpo8+1)
large rRNA BLAST databases distributed with the NCBI toolkit
ncbi-tools-bin (6.1.20170106-2~bpo8+1)
NCBI libraries for biology applications (text-based utilities)
ncbi-tools-x11 (6.1.20170106-2~bpo8+1)
NCBI libraries for biology applications (X-based utilities)
ncl-ncarg (6.3.0-4~bpo8+1)
NCAR Command Language and NCAR graphics
nco (4.6.3-1~bpo8+1)
Command-line operators to analyze netCDF files
ncview (2.1.7+ds-1~bpo8+1)
X11 visual browser for NetCDF format files
oce-draw (0.17.1-1~bpo8+1)
OpenCASCADE Community Edition CAE platform shared library
openfoam (4.0+dfsg1-7~bpo8+1)
Set of programs for Computational Fluid Dynamics (CFD). Binaries
openfoam-examples (4.0+dfsg1-7~bpo8+1)
Set of programs for Computational Fluid Dynamics (CFD). Examples
paraview (5.0.0+dfsg1-2~bpo8+1)
Program do wizualizacji równoległej
parsnp (1.2+dfsg-2~bpo8+1)
rapid core genome multi-alignment
pbbamtools (0.7.4+ds-1~bpo8+1)
processing Pacific Biosciences binary alignment/map files
pbbarcode (0.8.0-1~bpo8+1)
annotate PacBio sequencing reads with barcode information
pbdagcon (0.3+20161121+ds-1~bpo8+1 [amd64], 0~20151114+git1d12e13+ds-2~bpo8+1 [arm64, armel, i386, mipsel, ppc64el])
sequence consensus using directed acyclic graphs
pbgenomicconsensus (2.0.0+20151210-1~bpo8+1)
Pacific Biosciences variant and consensus caller
pbh5tools (0.8.0+dfsg-5~bpo8+1)
tools for manipulating Pacific Biosciences HDF5 files
pbhoney (15.8.24+dfsg-2~bpo8+1)
genomic structural variation discovery
pbjelly (15.8.24+dfsg-2~bpo8+1)
genome assembly upgrading tool
phipack (0.0.20160614-1~bpo8+1)
PHI test and other tests of recombination
phyml (3:3.2.0+dfsg-7~bpo8+1)
Phylogenetic estimation using Maximum Likelihood
picard-tools (2.1.1+dfsg-1~bpo8+1)
Command line tools to manipulate SAM and BAM files
pktools (2.6.7-2~bpo8+1)
GDAL add-on tools to perform useful raster processing
placnet (1.03-2~bpo8+1)
Plasmid Constellation Network project
plast (2.3.1+dfsg-2~bpo8+1)
Parallel Local Sequence Alignment Search Tool
plast-example (2.3.1+dfsg-2~bpo8+1)
Parallel Local Sequence Alignment Search Tool (example data)
plink1.9 (1.90~b3.45-170113-1~bpo8+1)
whole-genome association analysis toolset
poretools (0.5.1-1~bpo8+1)
toolkit for nanopore nucleotide sequencing data
pprepair (0.0~20150323-6284890-1~bpo8+1)
planar partition repair tool
prepair (0.7-2~bpo8+1)
polygon repair tool
prepair-data (0.7-2~bpo8+1)
polygon repair tool -- example data
prodigal (1:2.6.3-1~bpo8+1)
Microbial (bacterial and archaeal) gene finding program
proftmb (1.1.12-6~bpo8+1)
per-residue prediction of bacterial transmembrane beta barrels
progressivemauve (1.2.0+4713-1~bpo8+1)
multiple genome alignment algorithms
proj-rdnap (2008-4~bpo8+1) [non-free]
RDNAP grid correction files for PROJ.4
proteinortho (5.15+dfsg-1~bpo8+1)
Detection of (Co-)orthologs in large-scale protein analysis
prottest (3.4.2+dfsg-2~bpo8+2)
selection of best-fit models of protein evolution
pyfai (0.13.0+dfsg-1~bpo8+1)
Fast Azimuthal Integration scripts
pymol (1.8.4.0+dfsg-1~bpo8+1)
Molekularny system graficzny
pymol-data (1.8.4.0+dfsg-1~bpo8+1)
data files for PyMOL
qgis (2.14.11+dfsg-1~bpo8+1)
Geographic Information System (GIS)
qgis-common (2.14.11+dfsg-1~bpo8+1)
QGIS - architecture-independent data
qgis-plugin-globe (2.14.11+dfsg-1~bpo8+1)
OSG globe plugin for QGIS
qgis-plugin-globe-common (2.14.11+dfsg-1~bpo8+1)
OSG globe plugin for QGIS - architecture-independent data
qgis-plugin-grass (2.14.11+dfsg-1~bpo8+1)
GRASS plugin for QGIS
qgis-plugin-grass-common (2.14.11+dfsg-1~bpo8+1)
GRASS plugin for QGIS - architecture-independent data
qgis-provider-grass (2.14.11+dfsg-1~bpo8+1)
GRASS provider for QGIS
qgis-providers (2.14.11+dfsg-1~bpo8+1)
collection of data providers to QGIS
qgis-providers-common (2.14.11+dfsg-1~bpo8+1)
collection of data providers to QGIS - architecture-independent files
qgis-server (2.14.11+dfsg-1~bpo8+1)
QGIS server providing various OGC services
qlandkartegt (1.8.1+ds-1~bpo8+1)
GPS mapping (GeoTiff and vector) and GPSr management
qmapshack (1.7.2-1~bpo8+1)
GPS mapping (GeoTiff and vector) and GPSr management
raxml (8.2.9+dfsg-1~bpo8+1)
Randomized Axelerated Maximum Likelihood of phylogenetic trees
repeatmasker-recon (1.08-3~bpo8+1)
finds repeat families from biological sequences
rna-star (2.5.2b+dfsg-1~bpo8+1)
ultrafast universal RNA-seq aligner
roary (3.8.0+dfsg-1~bpo8+1)
high speed stand alone pan genome pipeline
saga (2.3.1+dfsg-3~bpo8+1)
System for Automated Geoscientific Analyses
saga-common (2.3.1+dfsg-3~bpo8+1)
SAGA GIS architecture independent files
saint (2.5.0+dfsg-2~bpo8+1)
Significance Analysis of INTeractome
samtools (1.3.1-2~bpo8+1)
processing sequence alignments in SAM and BAM formats
samtools-test (1.3.1-2~bpo8+1)
test files for the samtools package
seaview (1:4.6.1.2-2~bpo8+1)
Multiplatform interface for sequence alignment and phylogeny
seer (1.1.2-3~bpo8+1+b1)
genomic sequence element (kmer) enrichment analysis
seqan-apps (2.4.0+dfsg-8~bpo8+1 [amd64, arm64, armhf, i386, mips, mipsel, powerpc, s390x], 2.3.1+dfsg-4~bpo8+1 [ppc64el])
C++ library for the analysis of biological sequences
seqsero (1.0-2~bpo8+1)
Salmonella serotyping from genome sequencing data
sga (0.10.14-1~bpo8+1)
de novo genome assembler that uses string graphs
sickle (1.33-1~bpo8+1)
windowed adaptive trimming tool for FASTQ files using quality
sim4db (0~20150903+r2013-3~bpo8+1)
batch spliced alignment of cDNA sequences to a target genome
smithwaterman (0.0+20160702-1~bpo8+1)
determine similar regions between two strings or genomic sequences
smrtanalysis (0~20161126~bpo8+1)
software suite for single molecule, real-time sequencing
snakemake (3.9.0+dfsg-2~bpo8+1)
pythonic workflow management system
sniffles (1.0.1+ds-1~bpo8+1)
structural variation caller using third-generation sequencing
spades (3.9.0+dfsg-1~bpo8+1)
genome assembler for single-cell and isolates data sets
sprai (0.9.9.18+dfsg-1~bpo8+1)
single-pass sequencing read accuracy improver
spread-phy (1.0.7+dfsg-1~bpo8+1)
analyze and visualize phylogeographic reconstructions
sra-toolkit (2.8.1-2+dfsg-2~bpo8+1)
Narzędzia do Sequence Read Archive z NCBI
srst2 (0.2.0-4~bpo8+1)
Short Read Sequence Typing for Bacterial Pathogens
ssw-align (1.0-3~bpo8+1)
Smith-Waterman aligner based on libssw
stacks (1.44-2~bpo8+1)
pipeline for building loci from short-read DNA sequences
stacks-web (1.44-2~bpo8+1)
web interface for displaying loci from short-read sequences
subread (1.5.1+dfsg-4~bpo8+1)
toolkit for processing next-gen sequencing data
subread-data (1.5.1+dfsg-4~bpo8+1)
data files for subread package
sumo (0.28.0+dfsg1-1~bpo8+1)
Simulation of Urban MObility (SUMO)
sumo-tools (0.28.0+dfsg1-1~bpo8+1)
Simulation of Urban MObility (SUMO), tools and scripts
surankco (0.0.r5+dfsg-1~bpo8+1)
Supervised Ranking of Contigs in de novo Assemblies
survex (1.2.30-1~bpo8+1 [amd64, arm64, armel, armhf, i386, mips, mipsel, powerpc, ppc64el, s390x], 1.2.26-1~bpo8+1 [kfreebsd-amd64, kfreebsd-i386])
cave surveying and mapping software
survex-aven (1.2.30-1~bpo8+1 [amd64, arm64, armel, armhf, i386, mips, mipsel, powerpc, ppc64el, s390x], 1.2.26-1~bpo8+1 [kfreebsd-amd64, kfreebsd-i386])
sophisticated cave survey viewer for Survex
tabix (1.3.2-2~bpo8+1)
generic indexer for TAB-delimited genome position files
tantan (13-2~bpo8+1)
low complexity and tandem repeat masker for biosequences
theseus (3.3.0-5~bpo8+1)
superimpose macromolecules using maximum likelihood
theseus-examples (3.3.0-5~bpo8+1)
superimpose macromolecules using maximum likelihood (examples)
tophat (2.1.0+dfsg-1~bpo8+1)
fast splice junction mapper for RNA-Seq reads
trimmomatic (0.36+dfsg-1~bpo8+1)
flexible read trimming tool for Illumina NGS data
uhd-host (3.9.5-1~bpo8+1)
universal hardware driver for Ettus Research products - host apps
varscan (2.3.9+dfsg-1~bpo8+1) [non-free]
variant detection in next-generation sequencing data
vsearch (2.3.4-1~bpo8+1)
tool for processing metagenomic sequences
wcslib-tools (5.16-1~bpo8+1)
Command line tools utilizing wcslib
yade (2017.01a-7~bpo8+1 [amd64, arm64, i386, kfreebsd-amd64, powerpc, ppc64el, s390x], 1.20.0-2~bpo8+1 [armel, armhf, mips, mipsel])
Platform for discrete element modeling
yorick (2.2.04+dfsg1-2~bpo8+1)
Interpretowany język programowania oraz naukowy pakiet wizualizacyjny
yorick-data (2.2.04+dfsg1-2~bpo8+1)
interpreted library for the Yorick language
yorick-dev (2.2.04+dfsg1-2~bpo8+1)
development files for the Yorick interpreted language
yorick-full (2.2.04+dfsg1-2~bpo8+1)
full installation of the Yorick interpreter and add-ons
yorick-gyoto (1.0.1-3~bpo8+1)
General relativistic geodesic integration for the Yorick language
yorick-mpy-common (2.2.04+dfsg1-2~bpo8+1)
Message Passing Yorick (common files)
yorick-mpy-mpich2 (2.2.04+dfsg1-2~bpo8+1)
Message Passing Yorick (MPICH2 build)
yorick-mpy-openmpi (2.2.04+dfsg1-2~bpo8+1)
Message Passing Yorick (OpenMPI build)