med-bio

dep: [med-config] (= 3.9.0)

Debian Med general config package

dep: [med-tasks] (= 3.9.0)

Debian Med tasks for tasksel

rec: [abacas]

close gaps in genomic alignments from short reads

rec: [abpoa]

adaptive banded Partial Order Alignment

rec: [abyss]

de novo, parallel, sequence assembler for short reads

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: [any2fasta]

convert various sequence formats to FASTA

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: [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]

Bayesian MCMC phylogenetic inference

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: [bifrost]

parallel construction, indexing and querying of de Bruijn graphs

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: [btllib-tools]

Bioinformatics Technology Lab common code library tools

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: [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: [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]

Multiple alignment of nucleic acid and protein sequences (graphical interface)

rec: [cnvkit]

Copy number variant detection from targeted DNA sequencing

rec: [codonw]

Correspondence Analysis of Codon Usage

rec: [comet-ms]

Tandem mass spectrometry (MS/MS) search engine

rec: [concavity]

predictor of protein ligand binding sites from structure and conservation

rec: [conservation-code]

protein sequence conservation scoring tool

rec: [coot]

model building program for macromolecular crystallography

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: [ctffind]

fast and accurate defocus estimation from electron micrographs

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: [deblur]

deconvolution for Illumina amplicon sequencing

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: [dnarrange]

Method to find rearrangements in long DNA reads relative to a genome seq

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]

tools for searching collections of biological sequences

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: [fastq-pair]

Rewrites paired end fastq so all reads have a mate to separate out singletons

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: [flye]

de novo assembler for single molecule sequencing reads using repeat graphs

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: [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: genomicsdb-tools

Package not available

rec: [gentle]

suite for molecular cloning and sequence analysis

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: [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)

rec: [hyphy-pt]

Hypothesis testing using Phylogenies (pthreads version)

rec: [idba]

iterative De Bruijn Graph short read assemblers

rec: [igblast]

Immunoglobulin and T cell receptor variable domain sequence analysis

rec: [igor]

infers V(D)J recombination processes from sequencing data

rec: [igv]

Integrative Genomics Viewer

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: [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: [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: [lamassemble]

Merges overlapping "long" DNA reads into a consensus sequences

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: [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: [malt]

sequence alignment and analysis tool to process sequencing data

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 for massxpert -> massxpert2

rec: [mauve-aligner]

multiple genome alignment

rec: [mcaller]

find methylation in nanopore reads

rec: [mecat2]

ultra-fast and accurate de novo assembly tools for SMRT reads

rec: [megadepth]

computes coverage from BigWig and BAM sequencing files

rec: [megahit]

ultra-fast and memory-efficient meta-genome assembler

rec: [megan-ce]

interactive tool to explore and analyse microbiome sequencing data

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: [metaeuk]

sensitive, high-throughput gene discovery and annotation for metagenomics

rec: [metaphlan]

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: [minexpert2]

MS^n mass spectrometric data visualization and mining (runtime)

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: [mothur]

sequence analysis suite for research on microbiota

rec: [mptp]

single-locus species delimitation

rec: [mrbayes]

Bayesian Inference of Phylogeny

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

rec: [murasaki-mpi]

homology detection tool across multiple large genomes (MPI-version)

rec: [muscle]

Multiple alignment program of protein sequences

rec: [muscle3]

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: [nanopolish]

consensus caller for nanopore sequencing data

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: [ntcard]

Streaming algorithm to estimate cardinality in genomics datasets

rec: [nxtrim]

Optimized trimming of Illumina mate pair reads

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: [pbsim]

simulator for PacBio sequencing reads

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: [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: [provean]

Protein Variation Effect Analyzer

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: [pullseq]

Extract sequence from a fasta or fastq

rec: [pycoqc]

computes metrics and generates Interactive QC plots

rec: [pycorrfit]

tool for fitting correlation curves on a logarithmic plot

rec: [pyensembl]

installs data from the Ensembl genome database

rec: [pyfastx]

fast random access to sequences from FASTA/Q file - command

rec: [pymol]

Molecular Graphics System

rec: [pyscanfcs]

scientific tool for perpendicular line scanning FCS

rec: [python3-biomaj3-daemon]

BioMAJ daemon library

rec: [python3-bioxtasraw]

process biological small angle scattering data

rec: [python3-emperor]

visualizing high-throughput microbial community data

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: [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-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-megadepth]

BioCOnductor BigWig and BAM related utilities

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-kaos]

Encoding of Sequences Based on Frequency Matrix Chaos

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-treespace]

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]

tools for generating images of proteins or other molecules

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-readseq]

Ribosomal Database Project (RDP) sequence reading and writing

rec: [readseq]

Conversion between sequence formats

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]

toolkit for 3D reconstructions in cryo-electron microscopy (gui apps)

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: [rockhopper]

system for analyzing bacterial RNA-seq data

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: [sambamba]

tools for working with SAM/BAM 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: [savvy-util]

conversion tool for SAV file format

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]

Multiplatform interface for sequence alignment and phylogeny

rec: [seer]

genomic sequence element (kmer) enrichment analysis

rec: [segemehl]

short read mapping with gaps

rec: [seqan-apps]

C++ library for the analysis of biological sequences

rec: [seqan-needle]

pre-filter for the counting of very large collections of nucleotide sequences

rec: [seqan-raptor]

pre-filter for querying very large collections of nucleotide 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: [ska]

Split Kmer Analysis

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: [snippy]

rapid haploid variant calling and core genome alignment

rec: [snp-sites]

Binary code for the package snp-sites

rec: [snpeff]

genetic variant annotation and effect prediction toolbox - tool

rec: [snpomatic]

fast, stringent short-read mapping software

rec: [snpsift]

tool to annotate and manipulate genome variants - tool

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: [sourmash]

tools for comparing DNA sequences with MinHash sketches

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]

analyze and visualize phylogeographic reconstructions

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: [surpyvor]

modification of VCF files with SURVIVOR

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: [terraphast]

enumerate terraces in phylogenetic tree space

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: [tm-align]

structural alignment of proteins

rec: [tnseq-transit]

statistical calculations of essentiality of genes or genomic regions

rec: [toil]

cross-platform workflow engine

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

rec: [tree-ppuzzle]

Parallelized reconstruction of phylogenetic trees by maximum likelihood

rec: [treeview]

Java re-implementation of Michael Eisen's TreeView

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: [twopaco]

build the compacted de Bruijn graph from many complete genomes

rec: [uc-echo]

error correction algorithm designed for short-reads from NGS

rec: [ugene]

integrated bioinformatics toolkit

rec: [uncalled]

Utility for Nanopore Current Alignment to Large Expanses of DNA

rec: [unicycler]

hybrid assembly pipeline for bacterial genomes

rec: [unikmer]

Toolkit for nucleic acid k-mer analysis

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

rec: [velvet-long]

Nucleic acid sequence assembler for very short reads, long version

rec: [velvetoptimiser]

automatically optimise Velvet do novo assembly parameters

rec: [veryfasttree]

Speeding up the estimation of phylogenetic trees from sequences

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: [xpore]

Nanopore analysis of differential RNA modifications

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

sug: acacia

Package not available

sug: acedb-other

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: anfo

Package not available

sug: annovar

Package not available

sug: apollo

Package not available

sug: arachne

Package not available

sug: [arb]

phylogenetic sequence analysis suite - main program

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: ballview

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]

blocks database improved searcher

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: canu

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: circlator

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: copycat

Package not available

sug: covpipe

Package not available

sug: crossbow

Package not available

sug: crux-toolkit

Package not available

sug: [cufflinks]

Transcript assembly, differential expression and regulation for RNA-Seq

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: deepnano

Package not available

sug: dendroscope

Package not available

sug: diann

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: 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: ffp

Package not available

sug: fieldbioinformatics

Package not available

sug: figaro

Package not available

sug: flappie

Package not available

sug: forester

Package not available

sug: forge

Package not available

sug: galaxy

Package not available

sug: gamgi

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: hilive

Package not available

sug: htqc

Package not available

sug: hts-nim-tools

Package not available

sug: idefix

Package not available

sug: idseq-bench

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: jmodeltest

Package not available

sug: kempbasu

Package not available

sug: khmer

Package not available

sug: [libhdf5-dev]

HDF5 - development files - serial version

sug: [libhnswlib-dev]

fast approximate nearest neighbor search

sug: libpwiz-tools

Package not available

sug: lofreq

Package not available

sug: mach-haplotyper

Package not available

sug: mage2tab

Package not available

sug: maker2

Package not available

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: 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: mindthegap

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: mosdepth

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: nanook

Package not available

sug: nanoplot

Package not available

sug: nanostat

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: pbhoney

Package not available

sug: pbjelly

Package not available

sug: pbsuite

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: pplacer

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

Package not available

sug: [python3-cgecore]

Python3 module for the Center for Genomic Epidemiology

sug: python3-cogent3

Package not available

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-htseq]

Python3 high-throughput genome sequencing read analysis utilities

sug: python3-intake

Package not available

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

Package not available

sug: [python3-pyfaidx]

efficient random access to fasta subsequences for Python 3

sug: python3-pyflow

Package not available

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

Package not available

sug: q2-composition

Package not available

sug: q2-cutadapt

Package not available

sug: q2-dada2

Package not available

sug: q2-deblur

Package not available

sug: q2-demux

Package not available

sug: q2-diversity

Package not available

sug: q2-emperor

Package not available

sug: q2-feature-classifier

Package not available

sug: q2-feature-table

Package not available

sug: q2-fragment-insertion

Package not available

sug: q2-gneiss

Package not available

sug: q2-longitudinal

Package not available

sug: q2-metadata

Package not available

sug: q2-phylogeny

Package not available

sug: q2-quality-control

Package not available

sug: q2-quality-filter

Package not available

sug: q2-sample-classifier

Package not available

sug: q2-taxa

Package not available

sug: q2-types

Package not available

sug: q2-vsearch

Package not available

sug: q2cli

Package not available

sug: [q2templates]

Design template package for QIIME 2 Plugins

sug: qiime

Package not available

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-bitseq

Package not available

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-genabel

Package not available

sug: [r-cran-gprofiler2]

Interface to the 'g:Profiler' Toolset

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: raxml-ng

Package not available

sug: rbs-finder

Package not available

sug: rdp-classifier

Package not available

sug: readucks

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: sap

Package not available

sug: [science-workflow]

workflow management systems useful for scientific research

sug: sepp

Package not available

sug: [seq-gen]

simulate the evolution of nucleotide or amino acid sequences

sug: seq-seq-pan

Package not available

sug: [seqcluster]

analysis of small RNA in NGS data

sug: seqwish

Package not available

sug: [sift]

predicts if a substitution in a protein has a phenotypic effect

sug: signalalign

Package not available

sug: sina

Package not available

sug: sistr

Package not available

sug: situs

Package not available

sug: [solvate]

arranges water molecules around protein structures

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: tipp

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]

detection of transfer RNA genes in genomic sequence

sug: twain

Package not available

sug: ufasta

Package not available

sug: umap

Package not available

sug: umap-learn

Package not available

sug: umis

Package not available

sug: unc-fish

Package not available

sug: uniprime

Package not available

sug: varmatch

Package not available

sug: [varscan]

variant detection in next-generation sequencing data

sug: [vdjtools]

framework for post-analysis of B/T cell repertoires

sug: vg

Package not available

sug: [vienna-rna]

RNA sequence analysis

sug: viewmol

Package not available

sug: vmd

Package not available

sug: x-tandem-pipeline

Package not available

sug: zodiac-zeden

Package not available