Paketti: med-bio (3.3)

Links for med-bio

Debian-palvelut:

Imuroi lähdekoodipaketti debian-med:

Ylläpitäjät:

Samankaltaisia paketteja:

Debian Med bioinformatics packages

This metapackage will install Debian packages for use in molecular biology, structural biology and other biological sciences.

Tagit: Field: Biology, Role: Metapackage, Application Suite: Debian

Muut pakettiin med-bio liittyvät paketit

depends

recommends

suggests

enhances

dep: med-config (= 3.3)

Debian Med general config package
dep: med-tasks (= 3.3)

Debian Med tasks for tasksel

rec: abacas

close gaps in genomic alignments from short reads
rec: abyss

de novo, parallel, sequence assembler for short reads
rec: acedb-other

retrieval of DNA or protein sequences
rec: adapterremoval

rapid adapter trimming, identification, and read merging of gene sequences
rec: adun-core

Molecular Simulator
rec: aegean

integrated genome analysis toolkit
rec: aevol

digital genetics model to run Evolution Experiments in silico
rec: alien-hunter

Interpolated Variable Order Motifs to identify horizontally acquired DNA
rec: alter-sequence-alignment

genomic sequences ALignment Transformation EnviRonment
rec: altree

program to perform phylogeny-based association and localization analysis
rec: amap-align

Protein multiple alignment by sequence annealing
rec: ampliconnoise

removal of noise from 454 sequenced PCR amplicons
rec: andi

Efficient Estimation of Evolutionary Distances
rec: anfo

Short Read Aligner/Mapper from MPG
rec: aragorn

tRNA and tmRNA detection in nucleotide sequences
rec: arden

specificity control for read alignments using an artificial reference
rec: ariba

Antibiotic Resistance Identification By Assembly
rec: art-nextgen-simulation-tools

simulation tools to generate synthetic next-generation sequencing reads
rec: artemis

genome browser and annotation tool
rec: artfastqgenerator

outputs artificial FASTQ files derived from a reference genome
rec: assemblytics

detect and analyze structural variants from a genome assembly
rec: atac

genome assembly-to-assembly comparison
rec: augustus

gene prediction in eukaryotic genomes
rec: autodock

analysis of ligand binding to protein structure
rec: autodock-vina

docking of small molecules to proteins
rec: autogrid

pre-calculate binding of ligands to their receptor
rec: avogadro

Molecular Graphics and Modelling System
rec: axe-demultiplexer

Trie-based DNA sequencing read demultiplexer
rec: baitfisher

software package for designing hybrid enrichment probes
rec: bali-phy

Bayesian Inference of Alignment and Phylogeny
rec: ballview

free molecular modeling and molecular graphics tool
rec: bamtools

toolkit for manipulating BAM (genome alignment) files
rec: bandage

Bioinformatics Application for Navigating De novo Assembly Graphs Easily
rec: barrnap

rapid ribosomal RNA prediction
rec: bcbio

toolkit for analysing high-throughput sequencing data
rec: bcftools

genomic variant calling and manipulation of VCF/BCF files
rec: beads

2-DE electrophoresis gel image spot detection
rec: beagle

Genotype calling, genotype phasing and imputation of ungenotyped markers
rec: beast-mcmc

Bayesian MCMC phylogenetic inference
rec: beast2-mcmc

Bayesian MCMC phylogenetic inference
rec: bedops

high-performance genomic feature operations
rec: bedtools

suite of utilities for comparing genomic features
rec: belvu

multiple sequence alignment viewer and phylogenetic tool
rec: berkeley-express

Streaming quantification for high-throughput sequencing
rec: bio-eagle

Haplotype phasing within a genotyped cohort or using a phased reference panel
rec: bio-rainbow

clustering and assembling short reads for bioinformatics
rec: bio-tradis

analyse the output from TraDIS analyses of genomic sequences
rec: biosyntax

Syntax Highlighting for Computational Biology (metapackage)
rec: bitseq

Bayesian Inference of Transcripts from Sequencing Data
rec: blasr

mapping single-molecule sequencing reads
rec: blixem

interactive browser of sequence alignments
rec: bolt-lmm

Efficient large cohorts genome-wide Bayesian mixed-model association testing
rec: bowtie

Ultrafast memory-efficient short read aligner
rec: bowtie2

ultrafast memory-efficient short read aligner
rec: boxshade

Pretty-printing of multiple sequence alignments
rec: bppphyview

Bio++ Phylogenetic Viewer
rec: bppsuite

Bio++ program suite
rec: brig

BLAST Ring Image Generator
rec: bwa

Burrows-Wheeler Aligner
rec: canu

single molecule sequence assembler for genomes
rec: cassiopee

index and search tool in genomic sequences
rec: cct

visually comparing bacterial, plasmid, chloroplast, or mitochondrial sequences
rec: cd-hit

suite of programs designed to quickly group sequences
rec: cdbfasta

Constant DataBase indexing and retrieval tools for multi-FASTA files
rec: centrifuge

rapid and memory-efficient system for classification of DNA sequences
rec: cgview

Circular Genome Viewer
rec: changeo

Repertoire clonal assignment toolkit (Python 3)
rec: chimeraslayer

detects likely chimeras in PCR amplified DNA
rec: chromhmm

Chromatin state discovery and characterization
rec: chromimpute

Large-scale systematic epigenome imputation
rec: circlator

circularize genome assemblies
rec: circos

Plotteri visualisoimaan dataa
rec: clearcut

extremely efficient phylogenetic tree reconstruction
rec: clonalframe

inference of bacterial microevolution using multilocus sequence data
rec: clonalframeml

Efficient Inference of Recombination in Whole Bacterial Genomes
rec: clonalorigin

inference of homologous recombination in bacteria using whole genome sequences
rec: clustalo

General purpose multiple sequence alignment program for proteins
rec: clustalw

global multiple nucleotide or peptide sequence alignment
rec: clustalx

Multiple alignment of nucleic acid and protein sequences (graphical interface)
rec: cnvkit

Copy number variant detection from targeted DNA sequencing
rec: codonw

Correspondence Analysis of Codon Usage
rec: concavity

predictor of protein ligand binding sites from structure and conservation
rec: conservation-code

protein sequence conservation scoring tool
rec: crac

integrated RNA-Seq read analysis
rec: csb

Computational Structural Biology Toolbox (CSB)
rec: cutadapt

Clean biological sequences from high-throughput sequencing reads
rec: daligner

local alignment discovery between long nucleotide sequencing reads
rec: datamash

statistics tool for command-line interface
rec: dawg

simulate the evolution of recombinant DNA sequences
rec: dazzdb

manage nucleotide sequencing read data
rec: deepnano

alternative basecaller for MinION reads of genomic sequences
rec: delly

Structural variant discovery by read analysis
rec: dialign

Segment-based multiple sequence alignment
rec: dialign-tx

Segment-based multiple sequence alignment
rec: diamond-aligner

accelerated BLAST compatible local sequence aligner
rec: dindel

determines indel calls from short-read data
rec: discosnp

discovering Single Nucleotide Polymorphism from raw set(s) of reads
rec: disulfinder

cysteines disulfide bonding state and connectivity predictor
rec: dnaclust

tool for clustering millions of short DNA sequences
rec: dotter

detailed comparison of two genomic sequences
rec: dssp

protein secondary structure assignment based on 3D structure
rec: dwgsim

short sequencing read simulator
rec: e-mem

Efficient computation of Maximal Exact Matches for very large genomes
rec: ea-utils

command-line tools for processing biological sequencing data
rec: ecopcr

estimate PCR barcode primers quality
rec: edtsurf

triangulated mesh surfaces for protein structures
rec: eigensoft

reduction of population bias for genetic analyses
rec: elph

DNA/protein sequence motif finder
rec: embassy-domainatrix

Extra EMBOSS commands to handle domain classification file
rec: embassy-domalign

Extra EMBOSS commands for protein domain alignment
rec: embassy-domsearch

Extra EMBOSS commands to search for protein domains
rec: emboss

European molecular biology open software suite
rec: estscan

ORF-independent detector of coding DNA sequences
rec: examl

Exascale Maximum Likelihood (ExaML) code for phylogenetic inference
rec: exonerate

generic tool for pairwise sequence comparison
rec: fastahack

utility for indexing and sequence extraction from FASTA files
rec: fastaq

FASTA and FASTQ file manipulation tools
rec: fastdnaml

Tool for construction of phylogenetic trees of DNA sequences
rec: fastlink

faster version of pedigree programs of Linkage
rec: fastml

maximum likelihood ancestral amino-acid sequence reconstruction
rec: fastp

Ultra-fast all-in-one FASTQ preprocessor
rec: fastqc

quality control for high throughput sequence data
rec: fastqtl

Quantitative Trait Loci (QTL) mapper in cis for molecular phenotypes
rec: fasttree

phylogenetic trees from alignments of nucleotide or protein sequences
rec: fastx-toolkit

FASTQ/A short nucleotide reads pre-processing tools
rec: ffindex

simple index/database for huge amounts of small files
rec: figtree

graphical phylogenetic tree viewer
rec: fitgcp

fitting genome coverage distributions with mixture models
rec: flexbar

flexible barcode and adapter removal for sequencing platforms
rec: fml-asm

tool for assembling Illumina short reads in small regions
rec: freebayes

Bayesian haplotype-based polymorphism discovery and genotyping
rec: freecontact

fast protein contact predictor
rec: fsa

Fast Statistical Alignment of protein, RNA or DNA sequences
rec: fsm-lite

frequency-based string mining (lite)
rec: gamgi

General Atomistic Modelling Graphic Interface (GAMGI)
rec: garli

phylogenetic analysis of molecular sequence data using maximum-likelihood
rec: garlic

visualization program for biomolecules
rec: gasic

genome abundance similarity correction
rec: gatb-core

Genome Analysis Toolbox with de-Bruijn graph
rec: gbrowse

GMOD Generic Genome Browser
rec: gdpc

visualiser of molecular dynamic simulations
rec: gemma

Genome-wide Efficient Mixed Model Association
rec: genometester

toolkit for performing set operations on k-mer lists
rec: genometools

versatile genome analysis toolkit
rec: gentle

suite to plan genetic cloning
rec: gff2aplot

pair-wise alignment-plots for genomic sequences in PostScript
rec: gff2ps

produces PostScript graphical output from GFF-files
rec: ghemical

GNOME molecular modelling environment
rec: ghmm

General Hidden-Markov-Model library - tools
rec: giira

RNA-Seq driven gene finding incorporating ambiguous reads
rec: glam2

gapped protein motifs from unaligned sequences
rec: grabix

wee tool for random access into BGZF files
rec: graphlan

circular representations of taxonomic and phylogenetic trees
rec: grinder

Versatile omics shotgun and amplicon sequencing read simulator
rec: gromacs

Molecular dynamics simulator, with building and analysis tools
rec: gubbins

phylogenetic analysis of genome sequences
rec: gwama

Genome-Wide Association Meta Analysis
rec: harvest-tools

archiving and postprocessing for reference-compressed genomic multi-alignments
rec: hhsuite

sensitive protein sequence searching based on HMM-HMM alignment
rec: hilive

realtime alignment of Illumina reads
rec: hinge

long read genome assembler based on hinging
rec: hisat2

graph-based alignment of short nucleotide reads to many genomes
rec: hmmer

profile hidden Markov models for protein sequence analysis
rec: hmmer2

profile hidden Markov models for protein sequence analysis
rec: hyphy-mpi

Hypothesis testing using Phylogenies (MPI version)

tai hyphy-pt

Hypothesis testing using Phylogenies (pthreads version)
rec: idba

iterative De Bruijn Graph short read assemblers
rec: igor

infers V(D)J recombination processes from sequencing data
rec: indelible

powerful and flexible simulator of biological evolution
rec: infernal

inference of RNA secondary structural alignments
rec: ipig

integrating PSMs into genome browser visualisations
rec: iqtree

efficient phylogenetic software by maximum likelihood
rec: iva

iterative virus sequence assembler
rec: jaligner

Smith-Waterman algorithm with Gotoh's improvement
rec: jellyfish

count k-mers in DNA sequences
rec: jellyfish1

count k-mers in DNA sequences
rec: jmodeltest

HPC selection of models of nucleotide substitution
rec: jmol

Molecular Viewer
rec: kalign

Global and progressive multiple sequence alignment
rec: khmer

in-memory DNA sequence kmer counting, filtering & graph traversal
rec: kineticstools

detection of DNA modifications
rec: king-probe

Evaluate and visualize protein interatomic packing
rec: kissplice

Detection of various kinds of polymorphisms in RNA-seq data
rec: kmc

count kmers in genomic sequences
rec: kmer

suite of tools for DNA sequence analysis
rec: kraken

assigning taxonomic labels to short DNA sequences
rec: lagan

highly parametrizable pairwise global genome sequence aligner
rec: lamarc

Likelihood Analysis with Metropolis Algorithm using Random Coalescence
rec: lambda-align

Local Aligner for Massive Biological DatA
rec: lambda-align2

Local Aligner for Massive Biological DatA - v2
rec: last-align

genome-scale comparison of biological sequences
rec: leaff

biological sequence library utilities and applications
rec: lefse

determine features of organisms, clades, taxonomic units, genes
rec: librg-utils-perl

parsers and format conversion utilities used by (e.g.) profphd
rec: libvcflib-tools

C++ library for parsing and manipulating VCF files (tools)
rec: logol

Pattern matching tool using Logol language
rec: loki

MCMC-yhdistävä analysointi yleisille sukutauluille
rec: ltrsift

postprocessing and classification of LTR retrotransposons
rec: lucy

DNA sequence quality and vector trimming tool
rec: macs

Model-based Analysis of ChIP-Seq on short reads sequencers
rec: macsyfinder

detection of macromolecular systems in protein datasets
rec: maffilter

process genome alignment in the Multiple Alignment Format
rec: mafft

Multiple alignment program for amino acid or nucleotide sequences
rec: mapdamage

tracking and quantifying damage patterns in ancient DNA sequences
rec: mapsembler2

bioinformatics targeted assembly software
rec: maq

maps short fixed-length polymorphic DNA sequence reads to reference sequences
rec: maqview

graphical read alignment viewer for short gene sequences
rec: mash

fast genome and metagenome distance estimation using MinHash
rec: mauve-aligner

multiple genome alignment
rec: melting

compute the melting temperature of nucleic acid duplex
rec: meryl

in- and out-of-core kmer counting and utilities
rec: metaphlan2

Metagenomic Phylogenetic Analysis
rec: metastudent

predictor of Gene Ontology terms from protein sequence
rec: mhap

locality-sensitive hashing to detect long-read overlaps
rec: microbegps

explorative taxonomic profiling tool for metagenomic data
rec: microbiomeutil

Microbiome Analysis Utilities
rec: minia

short-read biological sequence assembler
rec: miniasm

ultrafast de novo assembler for long noisy DNA sequencing reads
rec: minimac4

Fast Imputation Based on State Space Reduction HMM
rec: minimap

tool for approximate mapping of long biosequences such as DNA reads
rec: minimap2

versatile pairwise aligner for genomic and spliced nucleotide sequences
rec: mipe

Tools to store PCR-derived data
rec: mira-assembler

Whole Genome Shotgun and EST Sequence Assembler
rec: mlv-smile

Find statistically significant patterns in sequences
rec: mothur

sequence analysis suite for research on microbiota
rec: mptp

single-locus species delimitation
rec: mrbayes

Bayesian Inference of Phylogeny
rec: mummer

Efficient sequence alignment of full genomes
rec: murasaki

homology detection tool across multiple large genomes

tai murasaki-mpi

homology detection tool across multiple large genomes (MPI-version)
rec: muscle

Multiple alignment program of protein sequences
rec: mustang

multiple structural alignment of proteins
rec: nanook

pre- and post-alignment analysis of nanopore sequencing data
rec: nanopolish

consensus caller for nanopore sequencing data
rec: nast-ier

NAST-based DNA alignment tool
rec: ncbi-blast+

next generation suite of BLAST sequence search tools
rec: ncbi-blast+-legacy

NCBI Blast legacy call script
rec: ncbi-entrez-direct

NCBI Entrez utilities on the command line
rec: ncbi-epcr

Tool to test a DNA sequence for the presence of sequence tagged sites
rec: ncbi-seg

tool to mask segments of low compositional complexity in amino acid sequences
rec: ncbi-tools-bin

NCBI libraries for biology applications (text-based utilities)
rec: ncbi-tools-x11

NCBI libraries for biology applications (X-based utilities)
rec: ncl-tools

tools to deal with NEXUS files
rec: ncoils

coiled coil secondary structure prediction
rec: neobio

computes alignments of amino acid and nucleotide sequences
rec: njplot

phylogenetic tree drawing program
rec: norsnet

tool to identify unstructured loops in proteins
rec: norsp

predictor of non-regular secondary structure
rec: obitools

programs to analyze NGS data in a DNA metabarcoding context
rec: openms

package for LC/MS data management and analysis
rec: pal2nal

converts proteins to genomic DNA alignment
rec: paleomix

pipelines and tools for the processing of ancient and modern HTS data
rec: paml

Phylogenetic Analysis by Maximum Likelihood (PAML)
rec: paraclu

Parametric clustering of genomic and transcriptomic features
rec: parsinsert

Parsimonious Insertion of unclassified sequences into phylogenetic trees
rec: parsnp

rapid core genome multi-alignment
rec: patman

rapid alignment of short sequences to large databases
rec: pbalign

map Pacific Biosciences reads to reference DNA sequences
rec: pbbarcode

annotate PacBio sequencing reads with barcode information
rec: pbdagcon

sequence consensus using directed acyclic graphs
rec: pbgenomicconsensus

Pacific Biosciences variant and consensus caller
rec: pbh5tools

tools for manipulating Pacific Biosciences HDF5 files
rec: pbhoney

genomic structural variation discovery
rec: pbjelly

genome assembly upgrading tool
rec: pbsim

simulator for PacBio sequencing reads
rec: pbsuite

software for Pacific Biosciences sequencing data
rec: pdb2pqr

Preparation of protein structures for electrostatics calculations
rec: perlprimer

Alukkeiden graafinen suunnittelu polymeraasiketjureaktiota varten
rec: perm

efficient mapping of short reads with periodic spaced seeds
rec: pftools

build and search protein and DNA generalized profiles
rec: phast

phylogenetic analysis with space/time models
rec: phipack

PHI test and other tests of recombination
rec: phybin

binning/clustering newick trees by topology
rec: phylip

package of programs for inferring phylogenies
rec: phyml

Phylogenetic estimation using Maximum Likelihood
rec: physamp

sample sequence alignment corresponding to phylogeny
rec: phyutility

simple analyses or modifications on both phylogenetic trees and data matrices
rec: phyx

UNIX-style phylogenetic analyses on trees and sequences
rec: picard-tools

Command line tools to manipulate SAM and BAM files
rec: piler

genomic repeat analysis
rec: pilon

automated genome assembly improvement and variant detection tool
rec: pirs

Profile based Illumina pair-end Reads Simulator
rec: placnet

Plasmid Constellation Network project
rec: plasmidomics

draw plasmids and vector maps with PostScript graphics export
rec: plasmidseeker

identification of known plasmids from whole-genome sequencing reads
rec: plast

Parallel Local Sequence Alignment Search Tool
rec: plink

whole-genome association analysis toolset
rec: plink1.9

whole-genome association analysis toolset
rec: plip

fully automated protein-ligand interaction profiler
rec: poa

Partial Order Alignment for multiple sequence alignment
rec: populations

population genetic software
rec: porechop

adapter trimmer for Oxford Nanopore reads
rec: poretools

toolkit for nanopore nucleotide sequencing data
rec: prank

Probabilistic Alignment Kit for DNA, codon and amino-acid sequences
rec: predictnls

prediction and analysis of protein nuclear localization signals
rec: predictprotein

suite of protein sequence analysis tools
rec: prime-phylo

bayesian estimation of gene trees taking the species tree into account
rec: primer3

tool to design flanking oligo nucleotides for DNA amplification
rec: proalign

Probabilistic multiple alignment program
rec: probabel

Toolset for Genome-Wide Association Analysis
rec: probalign

multiple sequence alignment using partition function posterior probabilities
rec: probcons

PROBabilistic CONSistency-based multiple sequence alignment
rec: proda

Proteiinisarjojen moninainen rivitys
rec: prodigal

Microbial (bacterial and archaeal) gene finding program
rec: profbval

predictor of flexible/rigid protein residues from sequence
rec: profisis

prediction of protein-protein interaction sites from sequence
rec: profnet-bval

neural network architecture for profbval
rec: profnet-chop

neural network architecture for profchop
rec: profnet-con

neural network architecture for profcon
rec: profnet-isis

neural network architecture for profisis
rec: profnet-md

neural network architecture for metadisorder
rec: profnet-norsnet

neural network architecture for norsnet
rec: profnet-prof

neural network architecture for profacc
rec: profnet-snapfun

neural network architecture for snapfun
rec: profphd

secondary structure and solvent accessibility predictor
rec: profphd-net

neural network architecture for profphd
rec: profphd-utils

profphd helper utilities convert_seq and filter_hssp
rec: proftmb

per-residue prediction of bacterial transmembrane beta barrels
rec: progressivemauve

multiple genome alignment algorithms
rec: proteinortho

Detection of (Co-)orthologs in large-scale protein analysis
rec: prottest

selection of best-fit models of protein evolution
rec: pscan-chip

ChIP-based identifcation of TF binding sites
rec: pscan-tfbs

search for transcription factor binding sites
rec: psortb

bacterial localization prediction tool
rec: pycorrfit

tool for fitting correlation curves on a logarithmic plot
rec: pymol

Molecular Graphics System
rec: pynast

alignment of short DNA sequences
rec: pyscanfcs

scientific tool for perpendicular line scanning FCS
rec: python-cogent

framework for genomic biology
rec: python3-biomaj3-daemon

BioMAJ daemon library
rec: python3-gffutils

Work with GFF and GTF files in a flexible database framework
rec: python3-presto

toolkit for processing B and T cell sequences
rec: python3-pybedtools

Python 3 wrapper around BEDTools for bioinformatics work
rec: python3-pybel

Biological Expression Language
rec: python3-sqt

SeQuencing Tools for biological DNA/RNA high-throughput data
rec: pyvcf

helper scripts for Variant Call Format (VCF) parser
rec: qcumber

quality control of genomic sequences
rec: qtltools

Tool set for molecular QTL discovery and analysis
rec: quorum

QUality Optimized Reads of genomic sequences
rec: qutemol

interactive visualization of macromolecules
rec: r-bioc-annotate

BioConductor annotation for microarrays
rec: r-bioc-biostrings

GNU R string objects representing biological sequences
rec: r-bioc-bitseq

transcript expression inference and analysis for RNA-seq data
rec: r-bioc-cner

CNE Detection and Visualization
rec: r-bioc-cummerbund

tool for analysis of Cufflinks RNA-Seq output
rec: r-bioc-deseq2

R package for RNA-Seq Differential Expression Analysis
rec: r-bioc-dnacopy

R package: DNA copy number data analysis
rec: r-bioc-ebseq

R package for RNA-Seq Differential Expression Analysis
rec: r-bioc-genefilter

methods for filtering genes from microarray experiments
rec: r-bioc-geneplotter

R package of functions for plotting genomic data
rec: r-bioc-gviz

Plotting data and annotation information along genomic coordinates
rec: r-bioc-hilbertvis

GNU R package to visualise long vector data
rec: r-bioc-impute

Imputation for microarray data
rec: r-bioc-limma

linear models for microarray data
rec: r-bioc-mergeomics

Integrative network analysis of omics data
rec: r-bioc-metagenomeseq

GNU R statistical analysis for sparse high-throughput sequencing
rec: r-bioc-pcamethods

BioConductor collection of PCA methods
rec: r-bioc-phyloseq

GNU R handling and analysis of high-throughput microbiome census data
rec: r-bioc-rtracklayer

GNU R interface to genome browsers and their annotation tracks
rec: r-bioc-tfbstools

GNU R Transcription Factor Binding Site (TFBS) Analysis
rec: r-cran-adegenet

GNU R exploratory analysis of genetic and genomic data
rec: r-cran-adephylo

GNU R exploratory analyses for the phylogenetic comparative method
rec: r-cran-alakazam

Immunoglobulin Clonal Lineage and Diversity Analysis
rec: r-cran-ape

GNU R package for Analyses of Phylogenetics and Evolution
rec: r-cran-bio3d

GNU R -paketti biologiseen rakenneanalyysiin
rec: r-cran-distory

GNU R distance between phylogenetic histories
rec: r-cran-genabel

GNU R package for genome-wide SNP association analysis
rec: r-cran-metamix

GNU R bayesian mixture analysis for metagenomic community profiling
rec: r-cran-phangorn

GNU R package for phylogenetic analysis
rec: r-cran-phytools

GNU R phylogenetic tools for comparative biology
rec: r-cran-pscbs

R package: Analysis of Parent-Specific DNA Copy Numbers
rec: r-cran-qtl

GNU R package for genetic marker linkage analysis
rec: r-cran-rotl

GNU R interface to the 'Open Tree of Life' API
rec: r-cran-samr

GNU R significance analysis of microarrays
rec: r-cran-sdmtools

Species Distribution Modelling Tools
rec: r-cran-seqinr

GNU R biological sequences retrieval and analysis
rec: r-cran-shazam

Immunoglobulin Somatic Hypermutation Analysis
rec: r-cran-tcr

Advanced Data Analysis of Immune Receptor Repertoires
rec: r-cran-tigger

Infers new Immunoglobulin alleles from Rep-Seq Data
rec: r-cran-treescape

GNU R Statistical Exploration of Landscapes of Phylogenetic Trees
rec: r-cran-vegan

Community Ecology Package for R
rec: r-other-hms-dbmi-spp

näennäispaketti, jonka toteuttaa r-cran-spp
rec: r-other-mott-happy.hbrem

GNU R package for fine-mapping complex diseases
rec: racon

consensus module for raw de novo DNA assembly of long uncorrected reads
rec: radiant

explore hierarchical metagenomic data with zoomable pie charts
rec: rambo-k

Read Assignment Method Based On K-mers
rec: rampler

module for sampling genomic sequences
rec: rapmap

rapid sensitive and accurate DNA read mapping via quasi-mapping
rec: rasmol

visualization of biological macromolecules
rec: raster3d

tools for generating images of proteins or other molecules
rec: rate4site

detector of conserved amino-acid sites
rec: raxml

Randomized Axelerated Maximum Likelihood of phylogenetic trees
rec: ray

de novo genome assemblies of next-gen sequencing data
rec: rdp-alignment

Ribosomal Database Project (RDP) alignment tools package
rec: rdp-classifier

extensible sequence classifier for fungal lsu, bacterial and archaeal 16s
rec: rdp-readseq

Ribosomal Database Project (RDP) sequence reading and writing
rec: readseq

Conversion between sequence formats
rec: reapr

universal tool for genome assembly evaluation
rec: relion-bin

toolkit for 3D reconstructions in cryo-electron microscopy

tai relion-bin+mpi

parallel toolkit for 3D reconstructions in cryo-electron microscopy
rec: relion-bin+gui

parallel toolkit for 3D reconstructions in cryo-electron microscopy

tai relion-bin+mpi+gui

parallel toolkit for 3D reconstructions in cryo-electron microscopy
rec: repeatmasker-recon

finds repeat families from biological sequences
rec: reprof

protein secondary structure and accessibility predictor
rec: rna-star

ultrafast universal RNA-seq aligner
rec: rnahybrid

Fast and effective prediction of microRNA/target duplexes
rec: roary

high speed stand alone pan genome pipeline
rec: roguenarok

versatile and scalable algorithm for rogue taxon identification
rec: rsem

RNA-Seq by Expectation-Maximization
rec: rtax

Classification of sequence reads of 16S ribosomal RNA gene
rec: runcircos-gui

GUI tool to run circos
rec: saint

Significance Analysis of INTeractome
rec: salmon

wicked-fast transcript quantification from RNA-seq data
rec: samblaster

marks duplicates, extracts discordant/split reads
rec: samtools

processing sequence alignments in SAM, BAM and CRAM formats
rec: scoary

pangenome-wide association studies
rec: scrm

simulator of evolution of genetic sequences
rec: scythe

Bayesian adaptor trimmer for sequencing reads
rec: seaview

Multiplatform interface for sequence alignment and phylogeny
rec: seer

genomic sequence element (kmer) enrichment analysis
rec: segemehl

short read mapping with gaps
rec: seqan-apps

C++ library for the analysis of biological sequences
rec: seqmagick

imagemagick-like frontend to Biopython SeqIO
rec: seqprep

stripping adaptors and/or merging paired reads of DNA sequences with overlap
rec: seqsero

Salmonella serotyping from genome sequencing data
rec: seqtk

Fast and lightweight tool for processing sequences in the FASTA or FASTQ format
rec: sga

de novo genome assembler that uses string graphs
rec: sibsim4

align expressed RNA sequences on a DNA template
rec: sickle

windowed adaptive trimming tool for FASTQ files using quality
rec: sigma-align

Simple greedy multiple alignment of non-coding DNA sequences
rec: sim4

Työkalu cDNA:n ja genomisen DNA:n rinnastamiseen
rec: sim4db

batch spliced alignment of cDNA sequences to a target genome
rec: smalr

interrogation of the methylation status of nucleotide sequencing reads
rec: smalt

Sequence Mapping and Alignment Tool
rec: smithwaterman

determine similar regions between two strings or genomic sequences
rec: snap

location of genes from DNA sequence with hidden markov model
rec: snap-aligner

Scalable Nucleotide Alignment Program
rec: sniffles

structural variation caller using third-generation sequencing
rec: snp-sites

Binary code for the package snp-sites
rec: snpomatic

fast, stringent short-read mapping software
rec: soapaligner

aligner of short reads of next generation sequencers
rec: soapdenovo

short-read assembly method to build de novo draft assembly
rec: soapdenovo2

short-read assembly method to build de novo draft assembly
rec: soapsnp

resequencing utility that can assemble consensus sequence of genomes
rec: sortmerna

tool for filtering, mapping and OTU-picking NGS reads
rec: spaced

alignment-free sequence comparison using spaced words
rec: spades

genome assembler for single-cell and isolates data sets
rec: spoa

SIMD partial order alignment tool
rec: sprai

single-pass sequencing read accuracy improver
rec: spread-phy

analyze and visualize phylogeographic reconstructions
rec: squizz

Converter for genetic sequences and alignments
rec: sra-toolkit

utilities for the NCBI Sequence Read Archive
rec: srst2

Short Read Sequence Typing for Bacterial Pathogens
rec: ssake

genomics application for assembling millions of very short DNA sequences
rec: sspace

scaffolding pre-assembled contigs after extension
rec: ssw-align

Smith-Waterman aligner based on libssw
rec: stacks

pipeline for building loci from short-read DNA sequences
rec: staden

DNA sequence assembly (Gap4/Gap5), editing and analysis tools
rec: staden-io-lib-utils

programs for manipulating DNA sequencing files
rec: subread

toolkit for processing next-gen sequencing data
rec: suitename

categorize each suite in an RNA backbone
rec: sumaclust

fast and exact clustering of genomic sequences
rec: sumatra

fast and exact comparison and clustering of sequences
rec: sumtrees

Phylogenetic Tree Summarization and Annotation
rec: surankco

Supervised Ranking of Contigs in de novo Assemblies
rec: swarm

robust and fast clustering method for amplicon-based studies
rec: sweed

assessment of SNPs for their evolutionary advantage
rec: t-coffee

Multiple Sequence Alignment
rec: tabix

generic indexer for TAB-delimited genome position files
rec: tantan

low complexity and tandem repeat masker for biosequences
rec: theseus

superimpose macromolecules using maximum likelihood
rec: tigr-glimmer

Gene detection in archea and bacteria
rec: tm-align

structural alignment of proteins
rec: tnseq-transit

statistical calculations of essentiality of genes or genomic regions
rec: toil

cross-platform workflow engine
rec: tophat

fast splice junction mapper for RNA-Seq reads
rec: topp

set of programs implementing The OpenMS Proteomic Pipeline
rec: toppred

transmembrane topology prediction
rec: trace2dbest

bulk submission of chromatogram data to dbEST
rec: tracetuner

interpretation of DNA Sanger sequencing data
rec: transdecoder

find coding regions within RNA transcript sequences
rec: transrate-tools

helper for transrate
rec: transtermhp

find rho-independent transcription terminators in bacterial genomes
rec: tree-puzzle

Reconstruction of phylogenetic trees by maximum likelihood

tai tree-ppuzzle

Parallelized reconstruction of phylogenetic trees by maximum likelihood
rec: treeview

Java re-implementation of Michael Eisen's TreeView
rec: treeviewx

Displays and prints phylogenetic trees
rec: trimmomatic

flexible read trimming tool for Illumina NGS data
rec: trinityrnaseq

RNA-Seq De novo Assembly
rec: tvc

genetic variant caller for Ion Torrent sequencing platforms
rec: uc-echo

error correction algorithm designed for short-reads from NGS
rec: unanimity

generate and process accurate consensus nucleotide sequences
rec: unicycler

hybrid assembly pipeline for bacterial genomes
rec: varna

Visualization Applet for RNA
rec: vcftools

Collection of tools to work with VCF files
rec: velvet

Nucleic acid sequence assembler for very short reads

tai velvet-long

Nucleic acid sequence assembler for very short reads, long version
rec: velvetoptimiser

automatically optimise Velvet do novo assembly parameters
rec: viewmol

graphical front end for computational chemistry programs
rec: vsearch

tool for processing metagenomic sequences
rec: wigeon

reimplementation of the Pintail 16S DNA anomaly detection utility
rec: wise

comparison of biopolymers, like DNA and protein sequences
rec: yaha

find split-read mappings on single-end queries
rec: zalign

parallel local alignment of biological sequences

sug: acacia

Paketti ei saatavilla
sug: adun.app

Molecular Simulator for GNUstep (GUI)
sug: amos-assembler

Paketti ei saatavilla
sug: amoscmp

Paketti ei saatavilla
sug: annovar

Paketti ei saatavilla
sug: apollo

Paketti ei saatavilla
sug: arachne

Paketti ei saatavilla
sug: arb

phylogenetic sequence analysis suite - main program
sug: asap

Paketti ei saatavilla
sug: atropos

Paketti ei saatavilla
sug: autodocktools

Paketti ei saatavilla
sug: axparafit

Paketti ei saatavilla
sug: axpcoords

Paketti ei saatavilla
sug: bagpipe

Paketti ei saatavilla
sug: bambus

Paketti ei saatavilla
sug: bax2bam

Paketti ei saatavilla
sug: biceps

Paketti ei saatavilla
sug: big-blast

Paketti ei saatavilla
sug: bigsdb

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sug: biobambam2

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sug: bismark

Paketti ei saatavilla
sug: blat

Paketti ei saatavilla
sug: blimps-utils

blocks database improved searcher
sug: blobology

Paketti ei saatavilla
sug: braker

Paketti ei saatavilla
sug: btk-core

Paketti ei saatavilla
sug: cactus

Paketti ei saatavilla
sug: caftools

Paketti ei saatavilla
sug: cain

simulations of chemical reactions
sug: card-rgi

Paketti ei saatavilla
sug: ccs

Paketti ei saatavilla
sug: cdna-db

Paketti ei saatavilla
sug: cellprofiler

Paketti ei saatavilla
sug: cinema

Paketti ei saatavilla
sug: cluster3

Reimplementation of the Eisen-clustering software
sug: cmap

Paketti ei saatavilla
sug: compclust

Paketti ei saatavilla
sug: condetri

Paketti ei saatavilla
sug: contrafold

Paketti ei saatavilla
sug: contralign

Paketti ei saatavilla
sug: coot

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sug: copycat

Paketti ei saatavilla
sug: crossbow

Paketti ei saatavilla
sug: crux-toolkit

Paketti ei saatavilla
sug: cufflinks

Transcript assembly, differential expression and regulation for RNA-Seq
sug: cytoscape

Paketti ei saatavilla
sug: dascrubber

alignment-based scrubbing pipeline for DNA sequencing reads
sug: dazzle

Paketti ei saatavilla
sug: deepbinner

Paketti ei saatavilla
sug: dendroscope

Paketti ei saatavilla
sug: e-hive

Paketti ei saatavilla
sug: ecell

Paketti ei saatavilla
sug: embassy-phylip

EMBOSS conversions of the programs in the phylip package
sug: emboss-explorer

web-based GUI to EMBOSS
sug: emmax

Paketti ei saatavilla
sug: emperor

Paketti ei saatavilla
sug: ensembl

Paketti ei saatavilla
sug: estferret

Paketti ei saatavilla
sug: euler-sr

Paketti ei saatavilla
sug: euler2

Paketti ei saatavilla
sug: exabayes

Paketti ei saatavilla
sug: exalt

Paketti ei saatavilla
sug: excavator

Paketti ei saatavilla
sug: falcon

Paketti ei saatavilla
sug: fasta3

tools for searching collections of biological sequences
sug: ffp

Paketti ei saatavilla
sug: figaro

Paketti ei saatavilla
sug: filtlong

Paketti ei saatavilla
sug: forester

Paketti ei saatavilla
sug: forge

Paketti ei saatavilla
sug: galaxy

Paketti ei saatavilla
sug: gassst

Paketti ei saatavilla
sug: gatk

Paketti ei saatavilla
sug: gbrowse-syn

Paketti ei saatavilla
sug: genemark

Paketti ei saatavilla
sug: genesplicer

Paketti ei saatavilla
sug: genetrack

Paketti ei saatavilla
sug: genezilla

Paketti ei saatavilla
sug: genographer

Paketti ei saatavilla
sug: getdata

management of external databases
sug: gffread

Paketti ei saatavilla
sug: glimmerhmm

Paketti ei saatavilla
sug: gmap

spliced and SNP-tolerant alignment for mRNA and short reads
sug: gmv

Paketti ei saatavilla
sug: gramalign

Paketti ei saatavilla
sug: haploview

Paketti ei saatavilla
sug: hawkeye

Paketti ei saatavilla
sug: htqc

Paketti ei saatavilla
sug: igdiscover

Paketti ei saatavilla
sug: igv

Paketti ei saatavilla
sug: inspect

Paketti ei saatavilla
sug: jalview

Paketti ei saatavilla
sug: jbrowse

Paketti ei saatavilla
sug: jigsaw

Paketti ei saatavilla
sug: kallisto

Paketti ei saatavilla
sug: kempbasu

Paketti ei saatavilla
sug: kma

Paketti ei saatavilla
sug: kmerresistance

Paketti ei saatavilla
sug: kraken2

Paketti ei saatavilla
sug: lofreq

Paketti ei saatavilla
sug: mach-haplotyper

Paketti ei saatavilla
sug: mage2tab

Paketti ei saatavilla
sug: maker2

Paketti ei saatavilla
sug: malt

Paketti ei saatavilla
sug: manta

Paketti ei saatavilla
sug: martj

Paketti ei saatavilla
sug: maude

high-performance logical framework
sug: maxd

Paketti ei saatavilla
sug: meme

Paketti ei saatavilla
sug: mesquite

Paketti ei saatavilla
sug: metabit

Paketti ei saatavilla
sug: metarep

Paketti ei saatavilla
sug: metastudent-data

predictor of Gene Ontology terms from protein sequence - data files
sug: metastudent-data-2

predictor of Gene Ontology terms from protein sequence - data #2
sug: metastudent-data-3

Paketti ei saatavilla
sug: mgltools-cadd

Computer Aided Drug Discovery (CADD) Pipeline
sug: mgltools-pmv

Paketti ei saatavilla
sug: mgltools-vision

Python-based Visual Programming Environment
sug: migrate

Paketti ei saatavilla
sug: minimus

Paketti ei saatavilla
sug: mirbase

Paketti ei saatavilla
sug: mirtop

Paketti ei saatavilla
sug: mobyle

Web portal that provides web forms for command-line software
sug: mobyle-programs

program descriptions for the mobyle portal
sug: mobyle-tutorials

program tutorials for the mobyle portal
sug: modeller

Paketti ei saatavilla
sug: molekel

Paketti ei saatavilla
sug: mosaik-aligner

Paketti ei saatavilla
sug: mosdepth

Paketti ei saatavilla
sug: mpsqed

Paketti ei saatavilla
sug: mrs

Information Retrieval System for Biomedical databanks
sug: msatfinder

Paketti ei saatavilla
sug: msxpertsuite

Paketti ei saatavilla
sug: mugsy

Paketti ei saatavilla
sug: multiqc

Paketti ei saatavilla
sug: mummergpu

Paketti ei saatavilla
sug: mview

Paketti ei saatavilla
sug: nanocall

Paketti ei saatavilla
sug: ncbi-igblast

Paketti ei saatavilla
sug: nextsv

Paketti ei saatavilla
sug: ngila

Paketti ei saatavilla
sug: ngsqctoolkit

Paketti ei saatavilla
sug: nw-align

Paketti ei saatavilla
sug: oases

Paketti ei saatavilla
sug: obo-edit

Paketti ei saatavilla
sug: oligoarrayaux

Paketti ei saatavilla
sug: omegamap

Paketti ei saatavilla
sug: oncofuse

Paketti ei saatavilla
sug: operondb

Paketti ei saatavilla
sug: optimir

Paketti ei saatavilla
sug: optitype

Paketti ei saatavilla
sug: paipline

Paketti ei saatavilla
sug: partigene

Paketti ei saatavilla
sug: partitionfinder

Paketti ei saatavilla
sug: patristic

Paketti ei saatavilla
sug: pcma

Paketti ei saatavilla
sug: pfaat

Paketti ei saatavilla
sug: phagefinder

Paketti ei saatavilla
sug: phpphylotree

Paketti ei saatavilla
sug: phylographer

Paketti ei saatavilla
sug: phylophlan

Paketti ei saatavilla
sug: phyloviz-core

Paketti ei saatavilla
sug: phylowin

Paketti ei saatavilla
sug: pilercr

Paketti ei saatavilla
sug: pipasic

Paketti ei saatavilla
sug: plato

Paketti ei saatavilla
sug: profit

Paketti ei saatavilla
sug: prokka

Paketti ei saatavilla
sug: prot4est

Paketti ei saatavilla
sug: psipred

Paketti ei saatavilla
sug: pssh2

Paketti ei saatavilla
sug: pyrophosphate-tools

Paketti ei saatavilla
sug: python-orange

Paketti ei saatavilla
sug: python-reaper

Paketti ei saatavilla
sug: python-treetime

Paketti ei saatavilla
sug: python3-geneimpacts

Paketti ei saatavilla
sug: qiime

Paketti ei saatavilla
sug: qtlcart

Paketti ei saatavilla
sug: qualimap

Paketti ei saatavilla
sug: quast

Paketti ei saatavilla
sug: r-bioc-annotationhub

GNU R client to access AnnotationHub resources
sug: r-bioc-aroma.light

BioConductor methods normalization and visualization of microarray data
sug: r-bioc-ensembldb

GNU R utilities to create and use an Ensembl based annotation database
sug: r-bioc-go.db

annotation maps describing the entire Gene Ontology
sug: r-bioc-savr

GNU R parse and analyze Illumina SAV files
sug: r-cran-boolnet

assembling, analyzing and visualizing Boolean networks
sug: r-cran-forecast

Paketti ei saatavilla
sug: r-cran-pheatmap

GNU R package to create pretty heatmaps
sug: r-cran-qqman

R package for visualizing GWAS results using Q-Q and manhattan plots
sug: r-cran-rentrez

GNU R interface to the NCBI's EUtils API
sug: r-cran-webgestaltr

Paketti ei saatavilla
sug: r-other-apmswapp

Paketti ei saatavilla
sug: raccoon

Paketti ei saatavilla
sug: ragout

Paketti ei saatavilla
sug: raxml-ng

Paketti ei saatavilla
sug: rbs-finder

Paketti ei saatavilla
sug: repeatmasker

Paketti ei saatavilla
sug: rmblast

Paketti ei saatavilla
sug: roadtrips

Paketti ei saatavilla
sug: roche454ace2caf

Paketti ei saatavilla
sug: rose

Paketti ei saatavilla
sug: rsat

Paketti ei saatavilla
sug: sailfish

Paketti ei saatavilla
sug: sambamba

Paketti ei saatavilla
sug: sap

Paketti ei saatavilla
sug: science-workflow

workflow management systems useful for scientific research
sug: seq-gen

simulate the evolution of nucleotide or amino acid sequences
sug: seq-seq-pan

Paketti ei saatavilla
sug: sequenceconverter.app

Paketti ei saatavilla
sug: sibelia

Paketti ei saatavilla
sug: sift

predicts if a substitution in a protein has a phenotypic effect
sug: sina

Paketti ei saatavilla
sug: sistr

Paketti ei saatavilla
sug: situs

Paketti ei saatavilla
sug: smrtanalysis

Paketti ei saatavilla
sug: snpeff

Paketti ei saatavilla
sug: solvate

arranges water molecules around protein structures
sug: sourmash

Paketti ei saatavilla
sug: spaln

Paketti ei saatavilla
sug: sparta

Paketti ei saatavilla
sug: splitstree

Paketti ei saatavilla
sug: ssaha

Paketti ei saatavilla
sug: strap

Paketti ei saatavilla
sug: strap-base

Paketti ei saatavilla
sug: stringtie

Paketti ei saatavilla
sug: tab2mage

Paketti ei saatavilla
sug: tacg

Paketti ei saatavilla
sug: taverna

Paketti ei saatavilla
sug: taxinspector

Paketti ei saatavilla
sug: tetra

Paketti ei saatavilla
sug: tide

Paketti ei saatavilla
sug: tigr-glimmer-mg

Paketti ei saatavilla
sug: tn-seqexplorer

Paketti ei saatavilla
sug: treebuilder3d

Paketti ei saatavilla
sug: treetime

Paketti ei saatavilla
sug: tripal

Paketti ei saatavilla
sug: trnascan-se

detection of transfer RNA genes in genomic sequence
sug: twain

Paketti ei saatavilla
sug: ugene

Paketti ei saatavilla
sug: umap

Paketti ei saatavilla
sug: umis

Paketti ei saatavilla
sug: unc-fish

Paketti ei saatavilla
sug: uniprime

Paketti ei saatavilla
sug: varmatch

Paketti ei saatavilla
sug: varscan

variant detection in next-generation sequencing data
sug: vcfanno

Paketti ei saatavilla
sug: vdjtools

Paketti ei saatavilla
sug: vienna-rna

Paketti ei saatavilla
sug: virulencefinder

Paketti ei saatavilla
sug: vmd

Paketti ei saatavilla
sug: x-tandem-pipeline

Paketti ei saatavilla
sug: zodiac-zeden

Paketti ei saatavilla

Imuroi med-bio

Imurointi kaikille saataville arkkitehtuureille
Arkkitehtuuri	Paketin koko	Koko asennettuna	Tiedostot
all	19.9 kt	48.0 kt	[tiedostoluettelo]