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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_3.7.1.dsc]
• [debian-med_3.7.1.tar.xz]

Maintainer:

• Debian Med Packaging Team (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 (= 3.7.1)

  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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