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[ Source: debian-med  ]

Links for med-bio

Trisquel Resources:

• Install using apturl
• Entry at directory.fsf.org
• Bug Reports
• Changelog
• Copyright File

Download Source Package debian-med:

• [debian-med_3.0.1ubuntu1.dsc]
• [debian-med_3.0.1ubuntu1.tar.xz]

Maintainer:

• Ubuntu Developers (Mail Archive)

Original Maintainers:

• Debian Med Packaging Team (Mail Archive)
• Andreas Tille

Similar packages:

• science-biology
• med-bio-dev
• med-typesetting
• med-config
• science-social
• science-dataacquisition
• science-imageanalysis
• science-electrophysiology
• med-imaging-dev
• science-dataacquisition-dev
• science-neuroscience-modeling

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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