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Package: med-bio (3.7.1)

Debian Med bioinformatics packages

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

Other Packages Related to med-bio

  • depends
  • recommends
  • suggests
  • dep: med-config (= 3.7.1)
    Debian Med general config package
  • dep: med-tasks (= 3.7.1)
    Debian Med tasks for tasksel
  • rec: abacas
    close gaps in genomic alignments from short reads
  • rec: abyss
    Package not available
  • 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: assembly-stats
    get assembly statistics from FASTA and FASTQ files
  • rec: assemblytics
    detect and analyze structural variants from a genome assembly
  • rec: atac
    genome assembly-to-assembly comparison
  • rec: ataqv
    ATAC-seq QC and visualization
  • rec: atropos
    NGS read trimming tool that is specific, sensitive, and speedy
  • rec: augur
    pipeline components for real-time virus analysis
  • 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: bamclipper
    Remove gene-specific primer sequences from SAM/BAM alignments
  • rec: bamkit
    tools for common BAM file manipulations
  • 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: bbmap
    BBTools genomic aligner and other tools for short sequences
  • rec: bcalm
    de Bruijn compaction in low memory
  • 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
    Package not available
  • 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: bio-vcf
    domain specific language (DSL) for processing the VCF format
  • rec: bioawk
    extension of awk for biological sequence analysis
  • rec: biobambam2
    tools for early stage alignment file processing
  • 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: busco
    benchmarking sets of universal single-copy orthologs
  • rec: bustools
    program for manipulating BUS files for single cell RNA-Seq datasets
  • rec: bwa
    Burrows-Wheeler Aligner
  • rec: canu
    single molecule sequence assembler for genomes
  • rec: cassiopee
    index and search tool in genomic sequences
  • rec: cat-bat
    taxonomic classification of contigs and metagenome-assembled genomes (MAGs)
  • 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: cif-tools
    Suite of tools to manipulate, validate and query mmCIF files
  • rec: circlator
    circularize genome assemblies
  • rec: circos
    plotter for visualizing data
  • 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
    Package not available
  • 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: covtobed
    convert the coverage track from a BAM file into a BED file
  • 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: cutesv
    comprehensive discovery of structural variations of genomic sequences
  • rec: daligner
    local alignment discovery between long nucleotide sequencing reads
  • rec: damapper
    long read to reference genome mapping tool
  • 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: density-fitness
    Calculates per-residue electron density scores
  • rec: dextractor
    (d)extractor and compression command library
  • 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: 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: drop-seq-tools
    analyzing Drop-seq data
  • 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: emmax
    genetic mapping considering population structure
  • 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: fasta3
    Package not available
  • rec: fastahack
    utility for indexing and sequence extraction from FASTA files
  • rec: fastani
    Fast alignment-free computation of whole-genome Average Nucleotide Identity
  • 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: ffindex
    simple index/database for huge amounts of small files
  • rec: figtree
    graphical phylogenetic tree viewer
  • rec: filtlong
    quality filtering tool for long reads of genome sequences
  • rec: fitgcp
    fitting genome coverage distributions with mixture models
  • rec: flash
    Fast Length Adjustment of SHort reads
  • 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: genomethreader
    software tool to compute gene structure predictions
  • rec: genometools
    versatile genome analysis toolkit
  • rec: gentle
    Package not available
  • rec: gff2aplot
    pair-wise alignment-plots for genomic sequences in PostScript
  • rec: gff2ps
    produces PostScript graphical output from GFF-files
  • rec: gffread
    GFF/GTF format conversions, region filtering, FASTA sequence extraction
  • rec: ggd-utils
    programs for use in ggd
  • rec: ghmm
    General Hidden-Markov-Model library - tools
  • rec: glam2
    gapped protein motifs from unaligned sequences
  • rec: gmap
    spliced and SNP-tolerant alignment for mRNA and short reads
  • 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: gsort
    sort genomic data
  • 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)
    or hyphy-pt
    Hypothesis testing using Phylogenies (pthreads version)
  • rec: idba
    iterative De Bruijn Graph short read assemblers
  • rec: igdiscover
    analyzes antibody repertoires to find new V genes
  • rec: igor
    infers V(D)J recombination processes from sequencing data
  • rec: igv
    Package not available
  • rec: indelible
    powerful and flexible simulator of biological evolution
  • rec: infernal
    inference of RNA secondary structural alignments
  • rec: insilicoseq
    sequencing simulator producing realistic Illumina reads
  • 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: jalview
    multiple alignment editor
  • 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: kallisto
    near-optimal RNA-Seq quantification
  • rec: kaptive
    obtain information about K and O types for Klebsiella genome assemblies
  • 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: kleborate
    tool to screen Klebsiella genome assemblies
  • rec: kma
    mapping genomic sequences to raw reads directly against redundant databases
  • rec: kmc
    count kmers in genomic sequences
  • rec: kmer
    suite of tools for DNA sequence analysis
  • rec: kmerresistance
    correlates mapped genes with the predicted species of WGS samples
  • rec: kraken
    assigning taxonomic labels to short DNA sequences
  • rec: kraken2
    taxonomic classification system using exact k-mer matches
  • 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: lastz
    pairwise aligning DNA 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: lighter
    fast and memory-efficient sequencing error corrector
  • rec: logol
    Pattern matching tool using Logol language
  • rec: loki
    MCMC linkage analysis on general pedigrees
  • rec: ltrsift
    postprocessing and classification of LTR retrotransposons
  • rec: lucy
    DNA sequence quality and vector trimming tool
  • rec: lumpy-sv
    general probabilistic framework for structural variant discovery
  • 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: mecat2
    ultra-fast and accurate de novo assembly tools for SMRT reads
  • rec: megahit
    ultra-fast and memory-efficient meta-genome assembler
  • rec: melting
    compute the melting temperature of nucleic acid duplex
  • rec: meryl
    in- and out-of-core kmer counting and utilities
  • rec: metabat
    robust statistical framework for reconstructing genomes from metagenomic data
  • 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: mindthegap
    performs detection and assembly of DNA insertion variants in NGS read datasets
  • 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: mirtop
    annotate miRNAs with a standard mirna/isomir naming
  • rec: mlv-smile
    Find statistically significant patterns in sequences
  • rec: mmb
    model the structure and dynamics of macromolecules
  • rec: mmseqs2
    ultra fast and sensitive protein search and clustering
  • rec: mosdepth
    Package not available
  • rec: mothur
    sequence analysis suite for research on microbiota
  • rec: mptp
    single-locus species delimitation
  • rec: mrbayes
    Bayesian Inference of Phylogeny
  • rec: msxpertsuite
    mass spectrometry software suite - metapackage
  • rec: multiqc
    output integration for RNA sequencing across tools and samples
  • rec: mummer
    Efficient sequence alignment of full genomes
  • rec: murasaki
    homology detection tool across multiple large genomes
    or 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: nanofilt
    filtering and trimming of long read sequencing data
  • rec: nanolyse
    remove lambda phage reads from a fastq file
  • rec: nanook
    pre- and post-alignment analysis of nanopore sequencing data
  • rec: nanopolish
    consensus caller for nanopore sequencing data
  • rec: nanostat
    statistics on long biological sequences
  • rec: nanosv
    structural variant caller for nanopore data
  • rec: nast-ier
    NAST-based DNA alignment tool
  • rec: ncbi-acc-download
    download genome files from NCBI by accession
  • 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: ngmlr
    CoNvex Gap-cost alignMents for Long Reads
  • 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: optimir
    Integrating genetic variations in miRNA alignment
  • 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: parasail
    Aligner based on libparasail
  • 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: pbdagcon
    sequence consensus using directed acyclic graphs
  • 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
    Graphical design of primers for PCR
  • 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: phylonium
    Fast and Accurate Estimation of Evolutionary Distances
  • 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: picopore
    lossless compression of Nanopore files
  • rec: pigx-rnaseq
    pipeline for checkpointed and distributed RNA-seq analyses
  • rec: piler
    genomic repeat analysis
  • rec: pilercr
    software for finding CRISPR repeats
  • rec: pilon
    automated genome assembly improvement and variant detection tool
  • rec: pinfish
    Collection of tools to annotate genomes using long read transcriptomics data
  • rec: pique
    software pipeline for performing genome wide association studies
  • rec: pirs
    Profile based Illumina pair-end Reads Simulator
  • rec: pizzly
    Identifies gene fusions in RNA sequencing data
  • rec: placnet
    Plasmid Constellation Network project
  • rec: plasmidid
    mapping-based, assembly-assisted plasmid identification tool
  • 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: plink2
    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: pplacer
    phylogenetic placement and downstream analysis
  • rec: prank
    Probabilistic Alignment Kit for DNA, codon and amino-acid sequences
  • rec: predictnls
    prediction and analysis of protein nuclear localization signals
  • rec: presto
    toolkit for processing B and T cell 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: prinseq-lite
    PReprocessing and INformation of SEQuence data (lite version)
  • 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
    multiple alignment of protein sequences
  • 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-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: prokka
    rapid annotation of prokaryotic genomes
  • 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: pycoqc
    computes metrics and generates Interactive QC plots
  • rec: pycorrfit
    tool for fitting correlation curves on a logarithmic plot
  • rec: pymol
    Molecular Graphics System
  • rec: pyscanfcs
    scientific tool for perpendicular line scanning FCS
  • rec: python3-biomaj3-daemon
    BioMAJ daemon library
  • rec: python3-geneimpacts
    wraps command line tools to assess variants in gene sequences
  • rec: python3-gffutils
    Work with GFF and GTF files in a flexible database framework
  • rec: python3-pairtools
    Framework to process sequencing data from a Hi-C experiment
  • rec: python3-pybedtools
    Python 3 wrapper around BEDTools for bioinformatics work
  • rec: python3-sqt
    SeQuencing Tools for biological DNA/RNA high-throughput data
  • rec: python3-treetime
    inference of time stamped phylogenies and ancestral reconstruction (Python 3)
  • rec: pyvcf
    helper scripts for Variant Call Format (VCF) parser
  • rec: qcat
    demultiplexing Oxford Nanopore reads from FASTQ files
  • rec: qcumber
    quality control of genomic sequences
  • rec: qiime
    Quantitative Insights Into Microbial Ecology
  • rec: qtltools
    Tool set for molecular QTL discovery and analysis
  • rec: quicktree
    Neighbor-Joining algorithm for phylogenies
  • 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-ebseq
    R package for RNA-Seq Differential Expression Analysis
  • rec: r-bioc-edger
    Empirical analysis of digital gene expression data in R
  • rec: r-bioc-genefilter
    methods for filtering genes from microarray experiments
  • rec: r-bioc-geoquery
    Get data from NCBI Gene Expression Omnibus (GEO)
  • rec: r-bioc-hilbertvis
    GNU R package to visualise long vector data
  • rec: r-bioc-htsfilter
    GNU R filter replicated high-throughput transcriptome sequencing 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-mofa
    Multi-Omics Factor Analysis (MOFA)
  • rec: r-bioc-multiassayexperiment
    Software for integrating multi-omics experiments in BioConductor
  • rec: r-bioc-mutationalpatterns
    GNU R comprehensive genome-wide analysis of mutational processes
  • 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-scater
    Single-Cell Analysis Toolkit for Gene Expression Data in R
  • 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 package for biological structure analysis
  • 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-kaos
    Encoding of Sequences Based on Frequency Matrix Chaos
  • 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-seurat
    Tools for Single Cell Genomics
  • rec: r-cran-shazam
    Immunoglobulin Somatic Hypermutation Analysis
  • rec: r-cran-spp
    GNU R ChIP-seq processing pipeline
  • 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-tsne
    t-distributed stochastic neighbor embedding for R (t-SNE)
  • rec: r-cran-vegan
    Community Ecology Package for R
  • rec: r-cran-webgestaltr
    find over-represented properties in gene lists
  • rec: r-cran-wgcna
    Weighted Correlation Network Analysis
  • rec: r-other-ascat
    Allele-Specific Copy Number Analysis of Tumours
  • rec: r-other-mott-happy.hbrem
    GNU R package for fine-mapping complex diseases
  • rec: r-other-rajewsky-dropbead
    Basic Exploration and Analysis of Drop-seq Data
  • 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: ragout
    Reference-Assisted Genome Ordering UTility
  • 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
    Package not available
  • 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: readucks
    Nanopore read de-multiplexer (read demux -> readux -> readucks, innit)
  • rec: reapr
    universal tool for genome assembly evaluation
  • rec: recan
    genetic distance plotting for recombination events analysis
  • rec: relion
    toolkit for 3D reconstructions in cryo-electron microscopy
  • rec: relion-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: resfinder
    identify acquired antimicrobial resistance genes
  • 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: salmid
    rapid Kmer based Salmonella identifier from sequence data
  • rec: salmon
    wicked-fast transcript quantification from RNA-seq data
  • rec: samblaster
    marks duplicates, extracts discordant/split reads
  • rec: samclip
    filter SAM file for soft and hard clipped alignments
  • rec: samtools
    processing sequence alignments in SAM, BAM and CRAM formats
  • rec: scoary
    pangenome-wide association studies
  • rec: scrappie
    basecaller for Nanopore sequencer
  • rec: scrm
    simulator of evolution of genetic sequences
  • rec: scythe
    Bayesian adaptor trimmer for sequencing reads
  • rec: seaview
    Package not available
  • rec: seer
    genomic sequence element (kmer) enrichment analysis
  • rec: segemehl
    short read mapping with gaps
  • rec: sepp
    phylogeny with ensembles of Hidden Markov Models
  • rec: seqan-apps
    C++ library for the analysis of biological sequences
  • rec: seqkit
    cross-platform and ultrafast toolkit for FASTA/Q file manipulation
  • 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: shasta
    nanopore whole genome assembly (binaries and scripts)
  • rec: shovill
    Assemble bacterial isolate genomes from Illumina paired-end reads
  • rec: sibelia
    comparative genomics tool
  • 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
    tool for aligning cDNA and genomic DNA
  • rec: sim4db
    batch spliced alignment of cDNA sequences to a target genome
  • rec: simka
    comparative metagenomics method dedicated to NGS datasets
  • rec: simkamin
    approximate comparative metagenomics method dedicated to NGS datasets
  • rec: skesa
    strategic Kmer extension for scrupulous assemblies
  • rec: skewer
    post-processing of high-throughput DNA sequence reads
  • rec: smalt
    Sequence Mapping and Alignment Tool
  • rec: smithwaterman
    determine similar regions between two strings or genomic sequences
  • rec: smrtanalysis
    software suite for single molecule, real-time sequencing
  • 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: spaln
    splicing-aware transcript-alignment to genomic DNA
  • rec: spoa
    SIMD partial order alignment tool
  • rec: sprai
    single-pass sequencing read accuracy improver
  • rec: spread-phy
    Package not available
  • 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: stringtie
    assemble short RNAseq reads to transcripts
  • 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: survivor
    tool set for simulating/evaluating SVs
  • rec: svim
    Structural variant caller for long sequencing reads
  • 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: thesias
    Testing Haplotype Effects In Association Studies
  • rec: tiddit
    structural variant calling
  • rec: tigr-glimmer
    Gene detection in archea and bacteria
  • rec: tipp
    tool for Taxonomic Identification and Phylogenetic Profiling
  • rec: tm-align
    structural alignment of proteins
  • rec: tnseq-transit
    statistical calculations of essentiality of genes or genomic regions
  • rec: toil
    Package not available
  • rec: tombo
    identification of modified nucleotides from raw nanopore sequencing data
  • rec: tophat-recondition
    post-processor for TopHat unmapped reads
  • rec: topp
    set of programs implementing The OpenMS Proteomic Pipeline
  • rec: toppred
    transmembrane topology prediction
  • rec: tortoize
    Application to calculate ramachandran z-scores
  • 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
    or tree-ppuzzle
    Parallelized reconstruction of phylogenetic trees by maximum likelihood
  • rec: treeview
    Package not available
  • rec: treeviewx
    Displays and prints phylogenetic trees
  • rec: trf
    locate and display tandem repeats in DNA sequences
  • rec: trim-galore
    automate quality and adapter trimming for DNA sequencing
  • 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: umap-learn
    Uniform Manifold Approximation and Projection
  • rec: umis
    tools for processing UMI RNA-tag data
  • rec: uncalled
    Utility for Nanopore Current Alignment to Large Expanses of DNA
  • rec: unicycler
    hybrid assembly pipeline for bacterial genomes
  • rec: varna
    Visualization Applet for RNA
  • rec: vcfanno
    annotate a VCF with other VCFs/BEDs/tabixed files
  • rec: vcftools
    Collection of tools to work with VCF files
  • rec: velvet
    Nucleic acid sequence assembler for very short reads
    or velvet-long
    Nucleic acid sequence assembler for very short reads, long version
  • rec: velvetoptimiser
    automatically optimise Velvet do novo assembly parameters
  • rec: vg
    tools for working with genome variation graphs
  • rec: virulencefinder
    identify virulence genes in total or partial sequenced isolates of bacteria
  • rec: vmatch
    large scale sequence analysis software
  • rec: vsearch
    tool for processing metagenomic sequences
  • rec: vt
    toolset for short variant discovery in genetic sequence data
  • rec: wham-align
    Wisconsin's High-Throughput Alignment Method
  • 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: yanagiba
    filter low quality Oxford Nanopore reads basecalled with Albacore
  • rec: yanosim
    read simulator nanopore DRS datasets
  • rec: zalign
    parallel local alignment of biological sequences
  • sug: acacia
    Package not available
  • sug: adun.app
    Molecular Simulator for GNUstep (GUI)
  • sug: agat
    Package not available
  • sug: amos-assembler
    Package not available
  • sug: amoscmp
    Package not available
  • sug: annovar
    Package not available
  • sug: apollo
    Package not available
  • sug: arachne
    Package not available
  • sug: arb
    Package not available
  • sug: arvados
    Package not available
  • sug: asap
    Package not available
  • sug: axparafit
    Package not available
  • sug: axpcoords
    Package not available
  • sug: bagpipe
    Package not available
  • sug: bambus
    Package not available
  • sug: bax2bam
    Package not available
  • sug: bcbio
    Package not available
  • sug: biceps
    Package not available
  • sug: big-blast
    Package not available
  • sug: bigsdb
    Package not available
  • sug: bismark
    Package not available
  • sug: blat
    Package not available
  • sug: blimps-utils
    Package not available
  • sug: blobology
    Package not available
  • sug: braker
    Package not available
  • sug: btk-core
    Package not available
  • sug: cactus
    Package not available
  • sug: caftools
    Package not available
  • sug: card-rgi
    Package not available
  • sug: catfishq
    concatenates fastq files
  • sug: cdna-db
    Package not available
  • sug: cellprofiler
    Package not available
  • sug: cinema
    Package not available
  • sug: cluster3
    Package not available
  • sug: cmap
    Package not available
  • sug: conda-package-handling
    create and extract conda packages of various formats
  • sug: condetri
    Package not available
  • sug: contrafold
    Package not available
  • sug: contralign
    Package not available
  • sug: coot
    Package not available
  • sug: copycat
    Package not available
  • sug: covpipe
    Package not available
  • sug: crossbow
    Package not available
  • sug: crux-toolkit
    Package not available
  • sug: cufflinks
    Package not available
  • sug: cytoscape
    Package not available
  • sug: dascrubber
    alignment-based scrubbing pipeline for DNA sequencing reads
  • sug: dazzle
    Package not available
  • sug: deepbinner
    Package not available
  • sug: dendroscope
    Package not available
  • sug: dnapi
    adapter prediction for small RNA sequencing - utils
  • sug: e-hive
    Package not available
  • sug: ecell
    Package not available
  • sug: embassy-phylip
    Package not available
  • sug: emboss-explorer
    web-based GUI to EMBOSS
  • sug: ensembl
    Package not available
  • sug: ensembl-vep
    Package not available
  • sug: epigrass
    Package not available
  • sug: estferret
    Package not available
  • sug: euler-sr
    Package not available
  • sug: euler2
    Package not available
  • sug: exabayes
    Package not available
  • sug: exalt
    Package not available
  • sug: excavator
    Package not available
  • sug: falcon
    Package not available
  • sug: ffp
    Package not available
  • sug: fieldbioinformatics
    Package not available
  • sug: figaro
    Package not available
  • sug: flappie
    Package not available
  • sug: flye
    Package not available
  • sug: forester
    Package not available
  • sug: forge
    Package not available
  • sug: galaxy
    Package not available
  • sug: gatk
    Package not available
  • sug: gbrowse-syn
    Package not available
  • sug: genemark
    Package not available
  • sug: genesplicer
    Package not available
  • sug: genetrack
    Package not available
  • sug: genezilla
    Package not available
  • sug: genographer
    Package not available
  • sug: gerp++
    Package not available
  • sug: getdata
    management of external databases
  • sug: ghemical
    Package not available
  • sug: glimmerhmm
    Package not available
  • sug: gmv
    Package not available
  • sug: gramalign
    Package not available
  • sug: graphbin
    Package not available
  • sug: graphmap2
    Package not available
  • sug: haploview
    Package not available
  • sug: hawkeye
    Package not available
  • sug: htqc
    Package not available
  • sug: hts-nim-tools
    Package not available
  • sug: idefix
    Package not available
  • sug: idseq-bench
    Benchmark generator for the IDseq Portal
  • sug: igblast
    Package not available
  • sug: illustrate
    cartoonish representations of large biological molecules
  • sug: inspect
    Package not available
  • sug: jbrowse
    Package not available
  • sug: jigsaw
    Package not available
  • sug: kempbasu
    Package not available
  • sug: libhdf5-dev
    HDF5 - development files - serial version
  • sug: libhnswlib-dev
    fast approximate nearest neighbor search
  • sug: lofreq
    Package not available
  • sug: mach-haplotyper
    Package not available
  • sug: mage2tab
    Package not available
  • sug: maker2
    Package not available
  • sug: malt
    sequence alignment and analysis tool to process sequencing data
  • sug: manta
    Package not available
  • sug: marginphase
    Package not available
  • sug: martj
    Package not available
  • sug: maude
    high-performance logical framework
  • sug: maxd
    Package not available
  • sug: mcaller
    find methylation in nanopore reads
  • sug: medaka
    Package not available
  • sug: meme
    Package not available
  • sug: mesquite
    Package not available
  • sug: metabit
    Package not available
  • sug: metarep
    Package not available
  • 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: migrate
    Package not available
  • sug: minimus
    Package not available
  • sug: mirbase
    Package not available
  • sug: modeller
    Package not available
  • sug: molekel
    Package not available
  • sug: mosaik-aligner
    Package not available
  • sug: mpsqed
    Package not available
  • sug: mrs
    Package not available
  • sug: msatfinder
    Package not available
  • sug: mugsy
    Package not available
  • sug: mummergpu
    Package not available
  • sug: mview
    Package not available
  • sug: nano-snakemake
    Package not available
  • sug: nanocall
    Package not available
  • sug: nanocomp
    Package not available
  • sug: nanoplot
    Package not available
  • sug: ncbi-magicblast
    Package not available
  • sug: nextsv
    Package not available
  • sug: ngila
    Package not available
  • sug: ngsqctoolkit
    Package not available
  • sug: nw-align
    Package not available
  • sug: oases
    Package not available
  • sug: obo-edit
    Package not available
  • sug: oligoarrayaux
    Package not available
  • sug: omegamap
    Package not available
  • sug: oncofuse
    Package not available
  • sug: operondb
    Package not available
  • sug: optitype
    Package not available
  • sug: paipline
    Package not available
  • sug: pangolin
    Package not available
  • sug: partigene
    Package not available
  • sug: partitionfinder
    Package not available
  • sug: patristic
    Package not available
  • sug: pcma
    Package not available
  • sug: pfaat
    Package not available
  • sug: phagefinder
    Package not available
  • sug: phpphylotree
    Package not available
  • sug: phylographer
    Package not available
  • sug: phylophlan
    Package not available
  • sug: phyloviz-core
    Package not available
  • sug: phylowin
    Package not available
  • sug: pigx-scrnaseq
    Package not available
  • sug: pipasic
    Package not available
  • sug: plato
    Package not available
  • sug: pomoxis
    Package not available
  • sug: profit
    Package not available
  • sug: profphd
    Package not available
  • sug: prot4est
    Package not available
  • sug: psipred
    Package not available
  • sug: pssh2
    Package not available
  • sug: pufferfish
    Package not available
  • sug: purple
    Package not available
  • sug: pyrophosphate-tools
    Package not available
  • sug: python3-alignlib
    edit and Hamming distances for biological sequences
  • sug: python3-anndata
    annotated gene by sample numpy matrix
  • sug: python3-cgecore
    Python3 module for the Center for Genomic Epidemiology
  • sug: python3-cogent3
    framework for genomic biology
  • sug: python3-cyvcf2
    VCF parser based on htslib (Python 3)
  • sug: python3-deeptools
    platform for exploring biological deep-sequencing data
  • sug: python3-deeptoolsintervals
    handlig GTF-like sequence-associated interal-annotation
  • sug: python3-emperor
    visualizing high-throughput microbial community data
  • sug: python3-htseq
    Python3 high-throughput genome sequencing read analysis utilities
  • sug: python3-intake
    lightweight package for finding and investigating data
  • sug: python3-loompy
    access loom formatted files for bioinformatics
  • sug: python3-nanoget
    extract information from Oxford Nanopore sequencing data and alignments
  • sug: python3-nanomath
    simple math function for other Oxford Nanopore processing scripts
  • sug: python3-ncls
    datastructure for interval overlap queries
  • sug: python3-orange
    Package not available
  • sug: python3-py2bit
    access to 2bit files
  • sug: python3-pybel
    Biological Expression Language
  • sug: python3-pychopper
    identify, orient and trim full-length Nanopore cDNA reads
  • sug: python3-pyfaidx
    efficient random access to fasta subsequences for Python 3
  • sug: python3-pyflow
    lightweight parallel task engine for Python
  • sug: python3-pyranges
    2D representation of genomic intervals and their annotations
  • sug: python3-pyrle
    run length arithmetic in Python
  • sug: python3-pysam
    interface for the SAM/BAM sequence alignment and mapping format (Python 3)
  • sug: python3-tinyalign
    numerical representation of differences between strings
  • sug: q2-alignment
    QIIME 2 plugin for generating and manipulating alignments
  • sug: q2-composition
    Package not available
  • sug: q2-cutadapt
    QIIME 2 plugin to work with adapters in sequence data
  • sug: q2-dada2
    QIIME 2 plugin to work with adapters in sequence data
  • sug: q2-deblur
    Package not available
  • sug: q2-demux
    QIIME 2 plugin for demultiplexing of sequence reads
  • sug: q2-diversity
    Package not available
  • sug: q2-emperor
    Package not available
  • sug: q2-feature-classifier
    QIIME 2 plugin supporting taxonomic classification
  • sug: q2-feature-table
    QIIME 2 plugin supporting operations on feature tables
  • sug: q2-fragment-insertion
    QIIME 2 plugin for fragment insertion
  • sug: q2-gneiss
    Package not available
  • sug: q2-longitudinal
    Package not available
  • sug: q2-metadata
    QIIME 2 plugin for working with and visualizing Metadata
  • sug: q2-phylogeny
    QIIME 2 plugin for phylogeny
  • sug: q2-quality-control
    QIIME 2 plugin for quality assurance of feature and sequence data
  • sug: q2-quality-filter
    QIIME2 plugin for PHRED-based filtering and trimming
  • sug: q2-sample-classifier
    QIIME 2 plugin for machine learning prediction of sample data
  • sug: q2-taxa
    QIIME 2 plugin for working with feature taxonomy annotations
  • sug: q2-types
    QIIME 2 plugin defining types for microbiome analysis
  • sug: q2-vsearch
    Package not available
  • sug: q2cli
    Package not available
  • sug: q2templates
    Design template package for QIIME 2 Plugins
  • sug: qtlcart
    Package not available
  • sug: qtlreaper
    Package not available
  • sug: qualimap
    Package not available
  • sug: quast
    Package not available
  • 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-beachmat
    I/O for several formats storing matrix data
  • sug: r-bioc-biocneighbors
    Nearest Neighbor Detection for Bioconductor Packages
  • sug: r-bioc-biocsingular
    Singular Value Decomposition for Bioconductor Packages
  • sug: r-bioc-ctc
    Cluster and Tree Conversion
  • sug: r-bioc-dnacopy
    R package: DNA copy number data analysis
  • sug: r-bioc-ensembldb
    GNU R utilities to create and use an Ensembl based annotation database
  • sug: r-bioc-experimenthub
    BioConductor client to access ExperimentHub resources
  • sug: r-bioc-geneplotter
    R package of functions for plotting genomic data
  • sug: r-bioc-genomicalignments
    BioConductor representation and manipulation of short genomic alignments
  • sug: r-bioc-genomicfiles
    Distributed computing by file or by range
  • sug: r-bioc-genomicranges
    BioConductor representation and manipulation of genomic intervals
  • sug: r-bioc-go.db
    annotation maps describing the entire Gene Ontology
  • sug: r-bioc-grohmm
    GRO-seq Analysis Pipeline
  • sug: r-bioc-gviz
    Plotting data and annotation information along genomic coordinates
  • sug: r-bioc-isoformswitchanalyzer
    Identify, Annotate and Visualize Alternative Splicing and
  • sug: r-bioc-mofa2
    Package not available
  • sug: r-bioc-org.hs.eg.db
    genome-wide annotation for Human
  • sug: r-bioc-org.mm.eg.db
    Package not available
  • sug: r-bioc-qusage
    qusage: Quantitative Set Analysis for Gene Expression
  • sug: r-bioc-savr
    GNU R parse and analyze Illumina SAV files
  • sug: r-bioc-singlecellexperiment
    S4 Classes for Single Cell Data
  • sug: r-bioc-structuralvariantannotation
    Variant annotations for structural variants
  • sug: r-bioc-tximport
    transcript-level estimates for biological sequencing
  • sug: r-cran-amap
    Another Multidimensional Analysis Package
  • sug: r-cran-biwt
    biweight mean vector and covariance and correlation
  • sug: r-cran-boolnet
    assembling, analyzing and visualizing Boolean networks
  • sug: r-cran-corrplot
    Visualization of a Correlation Matrix
  • sug: r-cran-drinsight
    Package not available
  • sug: r-cran-dynamictreecut
    Methods for Detection of Clusters in Hierarchical Clustering
  • sug: r-cran-epir
    GNU R Functions for analysing epidemiological data
  • sug: r-cran-fitdistrplus
    support fit of parametric distribution
  • sug: r-cran-forecast
    GNU R forecasting functions for time series and linear models
  • sug: r-cran-gprofiler
    Interface to the 'g:Profiler' Toolkit
  • sug: r-cran-minerva
    Maximal Information-Based Nonparametric Exploration
  • sug: r-cran-optimalcutpoints
    Computing Optimal Cutpoints in Diagnostic Tests
  • sug: r-cran-parmigene
    Parallel Mutual Information to establish Gene Networks
  • 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-rcpphnsw
    R bindings for a Library for Approximate Nearest Neighbors
  • sug: r-cran-rentrez
    GNU R interface to the NCBI's EUtils API
  • sug: r-cran-sctransform
    Variance Stabilizing Transformations for Single Cell UMI Data
  • sug: r-other-apmswapp
    Package not available
  • sug: r-other-fastbaps
    Package not available
  • sug: raccoon
    Package not available
  • sug: raxml-ng
    Package not available
  • sug: rbs-finder
    Package not available
  • sug: relion-cuda
    Package not available
  • sug: relion-gui-cuda
    Package not available
  • sug: repeatmasker
    Package not available
  • sug: resfinder-db
    ResFinder database is a curated database of acquired resistance genes
  • sug: roadtrips
    Package not available
  • sug: roche454ace2caf
    Package not available
  • sug: rosa
    Package not available
  • sug: rose
    Package not available
  • sug: rsat
    Package not available
  • sug: sailfish
    Package not available
  • sug: sambamba
    tools for working with SAM/BAM data
  • sug: sap
    Package not available
  • 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
    Package not available
  • sug: seqcluster
    Package not available
  • sug: sequenceconverter.app
    Package not available
  • sug: seqwish
    Package not available
  • sug: sift
    Package not available
  • sug: signalalign
    Package not available
  • sug: sina
    Package not available
  • sug: sistr
    Package not available
  • sug: situs
    Package not available
  • sug: snpeff
    genetic variant annotation and effect prediction toolbox - tool
  • sug: solvate
    Package not available
  • sug: sourmash
    Package not available
  • sug: sparta
    Package not available
  • sug: splitstree
    Package not available
  • sug: ssaha
    Package not available
  • sug: strap
    Package not available
  • sug: strap-base
    Package not available
  • sug: strelka
    Package not available
  • sug: tab2mage
    Package not available
  • sug: tacg
    Package not available
  • sug: tandem-genotypes
    Package not available
  • sug: taverna
    Package not available
  • sug: taxinspector
    Package not available
  • sug: tetra
    Package not available
  • sug: tide
    Package not available
  • sug: tigr-glimmer-mg
    Package not available
  • sug: tn-seqexplorer
    Package not available
  • sug: tophat
    Package not available
  • sug: treebuilder3d
    Package not available
  • sug: tripal
    Package not available
  • sug: trnascan-se
    Package not available
  • sug: twain
    Package not available
  • sug: ufasta
    Package not available
  • sug: ugene
    Package not available
  • sug: umap
    Package not available
  • sug: unc-fish
    Package not available
  • sug: uniprime
    Package not available
  • sug: varmatch
    Package not available
  • sug: varscan
    Package not available
  • sug: vdjtools
    Package not available
  • sug: vienna-rna
    Package not available
  • sug: viewmol
    graphical front end for computational chemistry programs
  • sug: vmd
    Package not available
  • sug: x-tandem-pipeline
    Package not available
  • sug: zodiac-zeden
    Package not available

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