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[ Source: debian-med  ]

Package: med-bio (3.0.1ubuntu1)

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 (= 3.0.1ubuntu1)
    Debian Med general config package
  • dep: med-tasks (= 3.0.1ubuntu1)
    Debian Med tasks for tasksel
  • rec: abacas
    Algorithm Based Automatic Contiguation of Assembled Sequences
  • rec: acedb-other
    retrieval of DNA or protein sequences
  • rec: acedb-other-belvu
    transitional package for belvu
    also a virtual package provided by belvu
  • rec: acedb-other-dotter
    transitional package for dotter
    also a virtual package provided by dotter
  • 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: 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: axe-demultiplexer
    Trie-based DNA sequencing read demultiplexer
  • rec: baitfisher
    software package for designing hybrid enrichment probes
  • rec: ballview
    free molecular modeling and molecular graphics tool
  • rec: bamtools
    toolkit for manipulating BAM (genome alignment) files
  • rec: barrnap
    rapid ribosomal RNA prediction
  • rec: bcftools
    genomic variant calling and manipulation of VCF/BCF files
  • rec: beagle
    Genotype calling, genotype phasing and imputation of ungenotyped markers
  • rec: beast2-mcmc
    Bayesian MCMC phylogenetic inference
  • rec: bedops
    high-performance genomic feature operations
  • rec: bedtools
    suite of utilities for comparing genomic features
  • 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: blasr
    mapping single-molecule sequencing reads
  • 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: brig
    BLAST Ring Image Generator
  • rec: bwa
    Burrows-Wheeler Aligner
  • 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: cgview
    Circular Genome Viewer
  • rec: chimeraslayer
    detects likely chimeras in PCR amplified DNA
  • 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: clustalo
    General purpose multiple sequence alignment program for proteins
  • rec: clustalw
    global multiple nucleotide or peptide sequence alignment
  • 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: cutadapt
    Clean biological sequences from high-throughput sequencing reads
  • rec: daligner
    local alignment discovery between long nucleotide sequencing reads
  • rec: dascrubber
    alignment-based scrubbing pipeline for DNA sequencing reads
  • rec: datamash
    statistics tool for command-line interface
  • rec: dawg
    program to 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: 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: dssp
    protein secondary structure assignment based on 3D structure
  • rec: dwgsim
    short sequencing read simulator
  • 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: 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: examl
    Exascale Maximum Likelihood (ExaML) code for phylogenetic inference
  • rec: exonerate
    generic tool for pairwise sequence comparison
  • rec: falcon
    diploid-aware genome assembly of single-molecule sequencing reads
  • 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: 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: filo
    virtual package provided by bedtools
  • 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: gbrowse
    GMOD Generic Genome Browser
  • rec: gdpc
    visualiser of molecular dynamic simulations
  • 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: ghemical
    GNOME molecular modelling environment
  • rec: giira
    RNA-Seq driven gene finding incorporating ambiguous reads
  • rec: glam2
    gapped protein motifs from unaligned sequences
  • 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: 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: hyphygui
    Hypothesis testing using Phylogenies (GTK+ gui)
  • rec: idba
    iterative De Bruijn Graph short read assemblers
  • 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: jalview
    multiple alignment editor
  • rec: jellyfish
    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: lambda-align
    Local Aligner for Massive Biological DatA
  • 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-bin
    Pattern matching tool using Logol language
  • rec: loki
    MCMC linkage analysis on general pedigrees
  • rec: ltrsift
    postprocessing and classification of LTR retrotransposons
  • rec: macs
    Model-based Analysis of ChIP-Seq on short reads sequencers
  • rec: macsyfinder
    detection of macromolecular systems in protein datasets
  • rec: maffilter
    Package not available
  • 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: massxpert
    transitional package
  • 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: minimap
    tool for approximate mapping of long biosequences such as DNA reads
  • 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
  • rec: muscle
    Multiple alignment program of protein sequences
  • rec: mustang
    multiple structural alignment of proteins
  • 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: openms
    Package not available
  • rec: paleomix
    pipelines and tools for the processing of ancient and modern HTS data
  • 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: 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
    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: 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: picard-tools
    Command line tools to manipulate SAM and BAM files
  • rec: piler
    genomic repeat analysis
  • 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: 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: 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
    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
    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: 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
    BioMAJ workflow management library
  • 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: r-bioc-annotate
    BioConductor annotation for microarrays
  • rec: r-bioc-biostrings
    GNU R string objects representing biological sequences
  • 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-edger
    Package not available
  • 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-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-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-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-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-phangorn
    GNU R package for phylogenetic analysis
  • 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-seqinr
    GNU R biological sequences retrieval and analysis
  • 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-mott-happy.hbrem
    GNU R package for fine-mapping complex diseases
  • rec: radiant
    explore hierarchical metagenomic data with zoomable pie charts
  • rec: rambo-k
    Read Assignment Method Based On K-mers
  • rec: rapmap
    rapid sensitive and accurate DNA read mapping via quasi-mapping
  • rec: rasmol
    Visualize biological macromolecules
  • 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
    or 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
    or 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: samtools
    processing sequence alignments in SAM and BAM formats
  • rec: scrm
    simulator of evolution of genetic sequences
  • rec: scythe
    Bayesian adaptor trimmer for sequencing reads
  • rec: seer
    genomic sequence element (kmer) enrichment analysis
  • rec: seq-gen
    simulate the evolution of nucleotide or amino acid sequences
  • rec: seqan-apps
    C++ library for the analysis of biological sequences
  • 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
    tool for aligning cDNA and genomic DNA
  • rec: sim4db
    batch spliced alignment of cDNA sequences to a target genome
  • 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: soapdenovo
    short-read assembly method to build de novo draft assembly
  • rec: soapdenovo2
    short-read assembly method to build de novo draft assembly
  • 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: sprai
    single-pass sequencing read accuracy improver
  • 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 maniuplating 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: 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: tophat
    fast splice junction mapper for RNA-Seq reads
  • rec: topp
    Package not available
  • rec: toppred
    transmembrane topology prediction
  • 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: treeviewx
    Displays and prints phylogenetic trees
  • rec: trimmomatic
    flexible read trimming tool for Illumina NGS data
  • rec: trinityrnaseq
    RNA-Seq De novo Assembly
  • rec: uc-echo
    error correction algorithm designed for short-reads from NGS
  • rec: ugene
    integrated bioinformatics toolkit
  • 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
    or velvet-long
    Nucleic acid sequence assembler for very short reads, long version
  • rec: velvetoptimiser
    automatically optimise Velvet do novo assembly parameters
  • 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: zalign
    parallel local alignment of biological sequences
  • sug: abyss
    Package not available
  • sug: acacia
    Package not available
  • sug: adun.app
    Molecular Simulator for GNUstep (GUI)
  • sug: amos-assembler
    Package not available
  • sug: amoscmp
    Package not available
  • sug: apollo
    Package not available
  • sug: arachne
    Package not available
  • sug: arb
    Package not available
  • sug: asap
    Package not available
  • sug: autodocktools
    Package not available
  • sug: axparafit
    Package not available
  • sug: axpcoords
    Package not available
  • sug: bagpipe
    Package not available
  • sug: bambus
    Package not available
  • sug: beads
    2-DE electrophoresis gel image spot detection
  • sug: beast-mcmc
    Package not available
  • sug: biceps
    Package not available
  • sug: big-blast
    Package not available
  • sug: bigsdb
    Package not available
  • sug: biomaj
    Package not available
  • sug: biomaj-watcher
    Package not available
  • sug: bitseq
    Bayesian Inference of Transcripts from Sequencing Data
  • sug: blat
    Package not available
  • sug: blimps-utils
    Package not available
  • sug: blixem
    interactive browser of sequence alignments
  • sug: blobology
    Package not available
  • sug: btk-core
    Package not available
  • sug: cactus
    Package not available
  • sug: caftools
    Package not available
  • sug: cain
    simulations of chemical reactions
  • sug: canu
    single molecule sequence assembler for genomes
  • sug: cap3
    Package not available
  • sug: ccs
    Package not available
  • sug: cdna-db
    Package not available
  • sug: cinema
    Package not available
  • sug: clonalorigin
    inference of homologous recombination in bacteria using whole genome sequences
  • sug: clustalx
    Package not available
  • sug: cluster3
    Package not available
  • sug: cmap
    Package not available
  • sug: cnvkit
    Package not available
  • sug: coalesce
    Package not available
  • sug: compclust
    Package not available
  • 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: crossbow
    Package not available
  • sug: crux-toolkit
    Package not available
  • sug: cufflinks
    Package not available
  • sug: cytoscape
    Package not available
  • sug: das-proserver
    Package not available
  • sug: dazzle
    Package not available
  • sug: decipher
    Package not available
  • sug: e-hive
    Package not available
  • sug: ecell
    Package not available
  • sug: eigensoft
    Package not available
  • sug: elph
    Package not available
  • sug: embassy-phylip
    Package not available
  • sug: emboss-explorer
    web-based GUI to EMBOSS
  • sug: emmax
    Package not available
  • sug: emperor
    Package not available
  • sug: ensembl
    Package not available
  • sug: est-db
    Package not available
  • sug: estferret
    Package not available
  • sug: estscan
    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: fasta
    Package not available
  • sug: fasta3
    Package not available
  • sug: ffp
    Package not available
  • sug: figaro
    Package not available
  • sug: finex
    Package not available
  • sug: fluctuate
    Package not available
  • sug: forester
    Package not available
  • sug: forge
    Package not available
  • sug: galaxy
    Package not available
  • sug: gassst
    Package not available
  • sug: gatk
    Package not available
  • sug: gbioseq
    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: gentle
    Package not available
  • sug: getdata
    management of external databases
  • sug: glimmerhmm
    Package not available
  • sug: gmap
    Package not available
  • sug: gmv
    Package not available
  • sug: grabix
    Package not available
  • sug: grogui
    Package not available
  • sug: haploview
    Package not available
  • sug: hawkeye
    Package not available
  • sug: hexamer
    Package not available
  • sug: hilbertvisgui
    Package not available
  • sug: htqc
    Package not available
  • sug: igv
    Package not available
  • sug: inspect
    Package not available
  • sug: jbrowse
    Package not available
  • sug: jigsaw
    Package not available
  • sug: jstreeview
    Package not available
  • sug: kclust
    Package not available
  • sug: kempbasu
    Package not available
  • sug: lagan
    Package not available
  • sug: lamarc
    Likelihood Analysis with Metropolis Algorithm using Random Coalescence
  • sug: lofreq
    Package not available
  • sug: logomat-m
    Package not available
  • sug: lucy
    Package not available
  • sug: mach-haplotyper
    Package not available
  • sug: mage2tab
    Package not available
  • sug: maker2
    Package not available
  • sug: malt
    Package not available
  • sug: manta
    Package not available
  • sug: martj
    Package not available
  • sug: maude
    high-performance logical framework
  • sug: maxd
    Package not available
  • sug: melting-gui
    graphical interface to compute the melting temperature of nucleic acid duplex
  • 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: metastudent-data-3
    Package not available
  • sug: mgltools-cadd
    Package not available
  • sug: mgltools-pmv
    Package not available
  • sug: mgltools-vision
    Package not available
  • sug: migrate
    Package not available
  • sug: minimus
    Package not available
  • sug: mirbase
    Package not available
  • 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
    Package not available
  • sug: molekel
    Package not available
  • sug: mosaik-aligner
    Package not available
  • sug: mpsqed
    Package not available
  • sug: mrs
    Information Retrieval System for Biomedical databanks
  • sug: msatfinder
    Package not available
  • sug: mugsy
    Package not available
  • sug: mummergpu
    Package not available
  • sug: mview
    Package not available
  • sug: nanocall
    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: obitools
    Package not available
  • sug: obo-edit
    Package not available
  • sug: oligoarrayaux
    Package not available
  • sug: omegamap
    Package not available
  • sug: operondb
    Package not available
  • sug: pal2nal
    Package not available
  • sug: paml
    Package not available
  • sug: partigene
    Package not available
  • sug: partitionfinder
    Package not available
  • sug: patman
    rapid alignment of short sequences to large databases
  • sug: patristic
    Package not available
  • sug: pcma
    Package not available
  • sug: pfaat
    Package not available
  • sug: phagefinder
    Package not available
  • sug: phast
    phylogenetic analysis with space/time models
  • 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: pipasic
    Package not available
  • sug: plato
    Package not available
  • sug: profit
    Package not available
  • sug: prokka
    Package not available
  • sug: prot4est
    Package not available
  • sug: pscan-tfbs
    Package not available
  • sug: psipred
    Package not available
  • sug: psortb
    bacterial localization prediction tool
  • sug: pssh2
    Package not available
  • sug: pyrophosphate-tools
    Package not available
  • sug: python-orange
    Package not available
  • sug: python-reaper
    Package not available
  • sug: qtlcart
    Package not available
  • sug: qualimap
    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-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-metamix
    Package not available
  • 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-other-apmswapp
    Package not available
  • sug: r-other-valdar-bagphenotype.library
    Package not available
  • sug: raccoon
    Package not available
  • sug: raster3d
    Package not available
  • sug: raxml-ng
    Package not available
  • sug: rbs-finder
    Package not available
  • sug: recombine
    Package not available
  • sug: repeatmasker
    Package not available
  • sug: rmblast
    Package not available
  • sug: roadtrips
    Package not available
  • sug: roche454ace2caf
    Package not available
  • sug: rose
    Package not available
  • sug: rosetta
    Package not available
  • sug: rsat
    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: seaview
    Package not available
  • sug: segemehl
    Package not available
  • sug: sequenceconverter.app
    Package not available
  • sug: sift
    Package not available
  • sug: situs
    Package not available
  • sug: snpeff
    Package not available
  • sug: sparta
    Package not available
  • sug: spice
    Package not available
  • sug: splitstree
    Package not available
  • sug: spread-phy
    Package not available
  • sug: ssaha
    Package not available
  • sug: strap
    Package not available
  • sug: strap-base
    Package not available
  • sug: tacg
    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: trace2dbest
    Package not available
  • sug: tracetuner
    Package not available
  • sug: treebuilder3d
    Package not available
  • sug: treetime
    Package not available
  • sug: treeview
    Package not available
  • sug: tripal
    Package not available
  • sug: trnascan-se
    Package not available
  • sug: tvc
    Package not available
  • sug: twain
    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: vienna-rna
    Package not available
  • sug: vmd
    Package not available
  • sug: x-tandem-pipeline
    Package not available
  • sug: zodiac-zeden
    Package not available

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