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[ Source: debian-med  ]

Paketti: med-cloud (3.0.1ubuntu1)

Debian Med bioinformatics applications usable in cloud computing

This metapackage will install Debian packages related to molecular biology, structural biology and bioinformatics for use in life sciences, that do not depend on graphical toolkits and therefore can fit on system images for use in cloud computing clusters, where space can be limited.

Muut pakettiin med-cloud liittyvät paketit

  • depends
  • recommends
  • suggests
  • dep: med-config (= 3.0.1ubuntu1)
    Debian Med general config package
  • dep: med-tasks (= 3.0.1ubuntu1)
    Debian Med tasks for tasksel
  • rec: acedb-other
    retrieval of DNA or protein sequences
  • rec: aevol
    digital genetics model to run Evolution Experiments in silico
  • rec: alien-hunter
    Interpolated Variable Order Motifs to identify horizontally acquired DNA
  • 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: 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: 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: bamtools
    toolkit for manipulating BAM (genome alignment) files
  • rec: bedtools
    suite of utilities for comparing genomic features
  • rec: biomaj
    Paketti ei saatavilla
  • rec: bioperl
    Perl tools for computational molecular biology
  • rec: bioperl-run
    BioPerl wrappers: scripts
  • rec: biosquid
    utilities for biological sequence analysis
  • rec: blast2
    transitional dummy package to ncbi-blast+-legacy
  • 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: bwa
    Burrows-Wheeler Aligner
  • rec: cain
    simulations of chemical reactions
  • rec: cassiopee
    index and search tool in genomic 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: circos
    plotter for visualizing data
  • rec: clearcut
    extremely efficient phylogenetic tree reconstruction
  • rec: clonalframe
    inference of bacterial microevolution using multilocus sequence data
  • rec: clustalo
    General purpose multiple sequence alignment program for proteins
  • rec: clustalw
    global multiple nucleotide or peptide sequence alignment
  • rec: concavity
    predictor of protein ligand binding sites from structure and conservation
  • rec: conservation-code
    protein sequence conservation scoring tool
  • rec: datamash
    statistics tool for command-line interface
  • rec: dialign
    Segment-based multiple sequence alignment
  • rec: dialign-tx
    Segment-based multiple sequence alignment
  • 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: dssp
    protein secondary structure assignment based on 3D structure
  • 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: exonerate
    generic tool for pairwise sequence comparison
  • rec: fastdnaml
    Tool for construction of phylogenetic trees of DNA sequences
  • rec: fastlink
    faster version of pedigree programs of Linkage
  • rec: fastqc
    quality control for high throughput sequence data
  • rec: fasttree
    phylogenetic trees from alignments of nucleotide or protein sequences
  • rec: fastx-toolkit
    FASTQ/A short nucleotide reads pre-processing tools
  • rec: filo
    näennäispaketti, jonka toteuttaa bedtools
  • rec: fitgcp
    fitting genome coverage distributions with mixture models
  • rec: flexbar
    flexible barcode and adapter removal for sequencing platforms
  • rec: freecontact
    fast protein contact predictor
  • rec: gasic
    genome abundance similarity correction
  • rec: genometools
    versatile genome analysis toolkit
  • rec: gff2aplot
    pair-wise alignment-plots for genomic sequences in PostScript
  • rec: gff2ps
    produces PostScript graphical output from GFF-files
  • rec: giira
    RNA-Seq driven gene finding incorporating ambiguous reads
  • rec: glam2
    gapped protein motifs from unaligned sequences
  • rec: grinder
    Versatile omics shotgun and amplicon sequencing read simulator
  • rec: gromacs
    Molecular dynamics simulator, with building and analysis tools
  • rec: hhsuite
    sensitive protein sequence searching based on HMM-HMM alignment
  • rec: hmmer
    profile hidden Markov models for protein sequence analysis
  • rec: idba
    iterative De Bruijn Graph short read assemblers
  • rec: infernal
    inference of RNA secondary structural alignments
  • rec: jellyfish
    count k-mers in DNA sequences
  • rec: kalign
    Global and progressive multiple sequence alignment
  • rec: kissplice
    Detection of various kinds of polymorphisms in RNA-seq data
  • rec: last-align
    genome-scale comparison of biological sequences
  • rec: loki
    MCMC linkage analysis on general pedigrees
  • rec: macs
    Model-based Analysis of ChIP-Seq on short reads sequencers
  • rec: mafft
    Multiple alignment program for amino acid or nucleotide sequences
  • rec: mapsembler2
    bioinformatics targeted assembly software
  • rec: maq
    maps short fixed-length polymorphic DNA sequence reads to reference sequences
  • rec: melting
    compute the melting temperature of nucleic acid duplex
  • rec: minia
    short-read biological sequence assembler
  • 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: mrbayes
    Bayesian Inference of Phylogeny
  • rec: mummer
    Efficient sequence alignment of full genomes
  • rec: muscle
    Multiple alignment program of protein sequences
  • rec: mustang
    multiple structural alignment of proteins
  • rec: ncbi-epcr
    Tool to test a DNA sequence for the presence of sequence tagged sites
  • rec: ncbi-tools-bin
    NCBI libraries for biology applications (text-based utilities)
  • rec: ncoils
    coiled coil secondary structure prediction
  • rec: neobio
    computes alignments of amino acid and nucleotide sequences
  • rec: paraclu
    Parametric clustering of genomic and transcriptomic features
  • rec: parsinsert
    Parsimonious Insertion of unclassified sequences into phylogenetic trees
  • rec: pdb2pqr
    Preparation of protein structures for electrostatics calculations
  • rec: perm
    efficient mapping of short reads with periodic spaced seeds
  • rec: phyml
    Phylogenetic estimation using Maximum Likelihood
  • rec: phyutility
    simple analyses or modifications on both phylogenetic trees and data matrices
  • rec: picard-tools
    Command line tools to manipulate SAM and BAM files
  • rec: plink
    whole-genome association analysis toolset
  • rec: poa
    Partial Order Alignment for multiple sequence alignment
  • rec: prank
    Probabilistic Alignment Kit for DNA, codon and amino-acid sequences
  • 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: probabel
    Toolset for Genome-Wide Association Analysis
  • rec: probcons
    PROBabilistic CONSistency-based multiple sequence alignment
  • rec: proda
    multiple alignment of protein sequences
  • rec: prodigal
    Microbial (bacterial and archaeal) gene finding program
  • rec: pynast
    alignment of short DNA sequences
  • rec: python-biopython
    Python library for bioinformatics (implemented in Python 2)
  • rec: python-cogent
    framework for genomic biology
  • rec: python3-biopython
    Python library for bioinformatics (implemented in Python 3)
  • rec: qiime
    Quantitative Insights Into Microbial Ecology
  • rec: r-bioc-edger
    Paketti ei saatavilla
  • rec: r-bioc-hilbertvis
    GNU R package to visualise long vector data
  • rec: r-cran-pvclust
    Paketti ei saatavilla
  • rec: r-cran-qtl
    GNU R package for genetic marker linkage analysis
  • rec: r-cran-vegan
    Community Ecology Package for R
  • rec: r-other-mott-happy.hbrem
    GNU R package for fine-mapping complex diseases
  • rec: readseq
    Conversion between sequence formats
  • rec: rnahybrid
    Fast and effective prediction of microRNA/target duplexes
  • rec: rtax
    Classification of sequence reads of 16S ribosomal RNA gene
  • rec: samtools
    processing sequence alignments in SAM and BAM formats
  • rec: seqan-apps
    C++ library for the analysis of biological sequences
  • rec: sibsim4
    align expressed RNA sequences on a DNA template
  • rec: sigma-align
    Simple greedy multiple alignment of non-coding DNA sequences
  • rec: sim4
    tool for aligning cDNA and genomic DNA
  • rec: smalt
    Sequence Mapping and Alignment Tool
  • rec: snap
    location of genes from DNA sequence with hidden markov model
  • 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: squizz
    Converter for genetic sequences and alignments
  • rec: sra-toolkit
    utilities for the NCBI Sequence Read Archive
  • rec: ssake
    genomics application for assembling millions of very short DNA sequences
  • rec: staden-io-lib-utils
    programs for maniuplating DNA sequencing files
  • rec: t-coffee
    Multiple Sequence Alignment
  • rec: tabix
    generic indexer for TAB-delimited genome position files
  • rec: theseus
    superimpose macromolecules using maximum likelihood
  • rec: tigr-glimmer
    Gene detection in archea and bacteria
  • rec: tophat
    fast splice junction mapper for RNA-Seq reads
  • rec: tree-puzzle
    Reconstruction of phylogenetic trees by maximum likelihood
    tai tree-ppuzzle
    Parallelized reconstruction of phylogenetic trees by maximum likelihood
  • rec: vcftools
    Collection of tools to work with VCF files
  • rec: velvet
    Nucleic acid sequence assembler for very short reads
  • rec: wise
    comparison of biopolymers, like DNA and protein sequences
  • rec: zalign
    parallel local alignment of biological sequences
  • sug: abyss
    Paketti ei saatavilla
  • sug: bagpipe
    Paketti ei saatavilla
  • sug: cufflinks
    Paketti ei saatavilla
  • sug: embassy-phylip
    Paketti ei saatavilla
  • sug: gmap
    Paketti ei saatavilla
  • sug: r-other-valdar-bagphenotype.library
    Paketti ei saatavilla
  • sug: raster3d
    Paketti ei saatavilla

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