Debian Med Project
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Summary
The Debian Med Pure Blend contains 883 packages which are grouped by metapackages. Each metapackage will cause the installation of packages for a specific topic. The following table lists the metapackages of Debian Med

Tasks page

This is a list of the Tasks Debian Med is made of:

Table of contents

Biology - Debian Med bioinformatics packages

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

Official Debian packages with high relevance

Abacas
Algorithm Based Automatic Contiguation of Assembled Sequences
Abyss
de novo, parallel, sequence assembler for short reads
Acedb-other
retrieval of DNA or protein sequences
Acedb-other-belvu
multiple sequence alignment editor
Acedb-other-dotter
visualisation of sequence similarity
Adapterremoval
rapid adapter trimming, identification, and read merging of gene sequences
Adun-core
Molecular Simulator
Aegean
integrated genome analysis toolkit
Aevol
digital genetics model to run Evolution Experiments in silico
Alien-hunter
Interpolated Variable Order Motifs to identify horizontally acquired DNA
Alter-sequence-alignment
genomic sequences ALignment Transformation EnviRonment
Altree
program to perform phylogeny-based association and localization analysis
Amap-align
Protein multiple alignment by sequence annealing
Ampliconnoise
removal of noise from 454 sequenced PCR amplicons
Andi
Efficient Estimation of Evolutionary Distances
Anfo
Short Read Aligner/Mapper from MPG
Aragorn
tRNA and tmRNA detection in nucleotide sequences
Arden
specificity control for read alignments using an artificial reference
Ariba
Antibiotic Resistance Identification By Assembly
Art-nextgen-simulation-tools
simulation tools to generate synthetic next-generation sequencing reads
Artemis
genome browser and annotation tool
Artfastqgenerator
outputs artificial FASTQ files derived from a reference genome
Atac
genome assembly-to-assembly comparison
Augustus
gene prediction in eukaryotic genomes
Autodock
analysis of ligand binding to protein structure
Autodock-vina
docking of small molecules to proteins
Autogrid
pre-calculate binding of ligands to their receptor
Axe-demultiplexer
Trie-based DNA sequencing read demultiplexer
Baitfisher
software package for designing hybrid enrichment probes
Ballview
free molecular modeling and molecular graphics tool
Bamtools
toolkit for manipulating BAM (genome alignment) files
Barrnap
rapid ribosomal RNA prediction
Bcftools
genomic variant calling and manipulation of VCF/BCF files
Beads
2-DE electrophoresis gel image spot detection
Beagle
Genotype calling, genotype phasing and imputation of ungenotyped markers
Beast-mcmc
Bayesian MCMC phylogenetic inference
Beast2-mcmc
Bayesian MCMC phylogenetic inference
Bedops
high-performance genomic feature operations
Bedtools
suite of utilities for comparing genomic features
Berkeley-express
Streaming quantification for high-throughput sequencing
Bio-eagle
Haplotype phasing within a genotyped cohort or using a phased reference panel
Bio-rainbow
clustering and assembling short reads for bioinformatics
Bio-tradis
analyse the output from TraDIS analyses of genomic sequences
Blasr
mapping single-molecule sequencing reads
Bowtie
Ultrafast memory-efficient short read aligner
Bowtie2
ultrafast memory-efficient short read aligner
Boxshade
Pretty-printing of multiple sequence alignments
Bppphyview
Bio++ Phylogenetic Viewer
Bppsuite
Bio++ program suite
Brig
BLAST Ring Image Generator
Bwa
Burrows-Wheeler Aligner
Canu
single molecule sequence assembler for genomes
Cassiopee
index and search tool in genomic sequences
Cd-hit
suite of programs designed to quickly group sequences
Cdbfasta
Constant DataBase indexing and retrieval tools for multi-FASTA files
Cgview
Circular Genome Viewer
Chimeraslayer
detects likely chimeras in PCR amplified DNA
Circlator
circularize genome assemblies
Circos
plotter for visualizing data
Clearcut
extremely efficient phylogenetic tree reconstruction
Clonalframe
inference of bacterial microevolution using multilocus sequence data
Clustalo
General purpose multiple sequence alignment program for proteins
Clustalw
global multiple nucleotide or peptide sequence alignment
Clustalx
Multiple alignment of nucleic acid and protein sequences (graphical interface)
Codonw
Correspondence Analysis of Codon Usage
Concavity
predictor of protein ligand binding sites from structure and conservation
Conservation-code
protein sequence conservation scoring tool
Crac
integrated RNA-Seq read analysis
Csb
Computational Structural Biology Toolbox (CSB)
Cutadapt
Clean biological sequences from high-throughput sequencing reads
Daligner
local alignment discovery between long nucleotide sequencing reads
Datamash
statistics tool for command-line interface
Dawg
program to simulate the evolution of recombinant DNA sequences
Dazzdb
manage nucleotide sequencing read data
Deepnano
alternative basecaller for MinION reads of genomic sequences
Dialign
Segment-based multiple sequence alignment
Dialign-tx
Segment-based multiple sequence alignment
Diamond-aligner
accelerated BLAST compatible local sequence aligner
Dindel
determines indel calls from short-read data
Discosnp
discovering Single Nucleotide Polymorphism from raw set(s) of reads
Disulfinder
cysteines disulfide bonding state and connectivity predictor
Dnaclust
tool for clustering millions of short DNA sequences
Dssp
protein secondary structure assignment based on 3D structure
Dwgsim
short sequencing read simulator
E-mem
Efficient computation of Maximal Exact Matches for very large genomes
Ea-utils
command-line tools for processing biological sequencing data
Ecopcr
estimate PCR barcode primers quality
Edtsurf
triangulated mesh surfaces for protein structures
Eigensoft
reduction of population bias for genetic analyses
Embassy-domainatrix
Extra EMBOSS commands to handle domain classification file
Embassy-domalign
Extra EMBOSS commands for protein domain alignment
Embassy-domsearch
Extra EMBOSS commands to search for protein domains
Emboss
European molecular biology open software suite
Examl
Exascale Maximum Likelihood (ExaML) code for phylogenetic inference
Exonerate
generic tool for pairwise sequence comparison
Falcon
diploid-aware genome assembly of single-molecule sequencing reads
Fastahack
utility for indexing and sequence extraction from FASTA files
Fastaq
FASTA and FASTQ file manipulation tools
Fastdnaml
Tool for construction of phylogenetic trees of DNA sequences
Fastlink
faster version of pedigree programs of Linkage
Fastml
maximum likelihood ancestral amino-acid sequence reconstruction
Fastqc
quality control for high throughput sequence data
Fastqtl
Quantitative Trait Loci (QTL) mapper in cis for molecular phenotypes
Fasttree
phylogenetic trees from alignments of nucleotide or protein sequences
Fastx-toolkit
FASTQ/A short nucleotide reads pre-processing tools
Ffindex
simple index/database for huge amounts of small files
Figtree
graphical phylogenetic tree viewer
Filo
FILe and stream Operations
Fitgcp
fitting genome coverage distributions with mixture models
Flexbar
flexible barcode and adapter removal for sequencing platforms
Fml-asm
tool for assembling Illumina short reads in small regions
Freebayes
Bayesian haplotype-based polymorphism discovery and genotyping
Freecontact
fast protein contact predictor
Fsa
Fast Statistical Alignment of protein, RNA or DNA sequences
Fsm-lite
frequency-based string mining (lite)
Gamgi
General Atomistic Modelling Graphic Interface (GAMGI)
Garli
phylogenetic analysis of molecular sequence data using maximum-likelihood
Garlic
A visualization program for biomolecules
Gasic
genome abundance similarity correction
Gbrowse
GMOD Generic Genome Browser
Gdpc
visualiser of molecular dynamic simulations
Genometools
versatile genome analysis toolkit
Gentle
suite to plan genetic cloning
Gff2aplot
pair-wise alignment-plots for genomic sequences in PostScript
Gff2ps
produces PostScript graphical output from GFF-files
Ghemical
GNOME molecular modelling environment
Giira
RNA-Seq driven gene finding incorporating ambiguous reads
Glam2
gapped protein motifs from unaligned sequences
Graphlan
circular representations of taxonomic and phylogenetic trees
Grinder
Versatile omics shotgun and amplicon sequencing read simulator
Gromacs
Molecular dynamics simulator, with building and analysis tools
Gubbins
phylogenetic analysis of genome sequences
Gwama
Genome-Wide Association Meta Analysis
Harvest-tools
archiving and postprocessing for reference-compressed genomic multi-alignments
Hhsuite
sensitive protein sequence searching based on HMM-HMM alignment
Hilive
realtime alignment of Illumina reads
Hisat2
graph-based alignment of short nucleotide reads to many genomes
Hmmer
profile hidden Markov models for protein sequence analysis
Hmmer2
profile hidden Markov models for protein sequence analysis
Hyphy-mpi
Hypothesis testing using Phylogenies (MPI version)
Hyphy-pt
Hypothesis testing using Phylogenies (pthreads version)
Hyphygui
Hypothesis testing using Phylogenies (GTK+ gui)
Idba
iterative De Bruijn Graph short read assemblers
Indelible
powerful and flexible simulator of biological evolution
Infernal
inference of RNA secondary structural alignments
Ipig
integrating PSMs into genome browser visualisations
Iqtree
efficient phylogenetic software by maximum likelihood
Iva
iterative virus sequence assembler
Jaligner
Smith-Waterman algorithm with Gotoh's improvement
Jalview
multiple alignment editor
Jellyfish
count k-mers in DNA sequences
Jmodeltest
HPC selection of models of nucleotide substitution
Jmol
Molecular Viewer
Kalign
Global and progressive multiple sequence alignment
Khmer
in-memory DNA sequence kmer counting, filtering & graph traversal
Kineticstools
detection of DNA modifications
King-probe
Evaluate and visualize protein interatomic packing
Kissplice
Detection of various kinds of polymorphisms in RNA-seq data
Kmc
count kmers in genomic sequences
Kmer
suite of tools for DNA sequence analysis
Kraken
assigning taxonomic labels to short DNA sequences
Lambda-align
Local Aligner for Massive Biological DatA
Last-align
genome-scale comparison of biological sequences
Leaff
biological sequence library utilities and applications
Lefse
determine features of organisms, clades, taxonomic units, genes
Librg-utils-perl
parsers and format conversion utilities used by (e.g.) profphd
Libvcflib-tools
C++ library for parsing and manipulating VCF files (tools)
Logol-bin
Pattern matching tool using Logol language
Loki
MCMC linkage analysis on general pedigrees
Ltrsift
postprocessing and classification of LTR retrotransposons
Macs
Model-based Analysis of ChIP-Seq on short reads sequencers
Macsyfinder
detection of macromolecular systems in protein datasets
Maffilter
process genome alignment in the Multiple Alignment Format
Mafft
Multiple alignment program for amino acid or nucleotide sequences
Mapdamage
tracking and quantifying damage patterns in ancient DNA sequences
Mapsembler2
bioinformatics targeted assembly software
Maq
maps short fixed-length polymorphic DNA sequence reads to reference sequences
Maqview
graphical read alignment viewer for short gene sequences
Mash
fast genome and metagenome distance estimation using MinHash
Massxpert
transitional package
Mauve-aligner
multiple genome alignment
Melting
compute the melting temperature of nucleic acid duplex
Meryl
in- and out-of-core kmer counting and utilities
Metaphlan2
Metagenomic Phylogenetic Analysis
Metastudent
predictor of Gene Ontology terms from protein sequence
Mhap
locality-sensitive hashing to detect long-read overlaps
Microbegps
explorative taxonomic profiling tool for metagenomic data
Microbiomeutil
Microbiome Analysis Utilities
Minia
short-read biological sequence assembler
Miniasm
ultrafast de novo assembler for long noisy DNA sequencing reads
Minimap
tool for approximate mapping of long biosequences such as DNA reads
Mipe
Tools to store PCR-derived data
Mira-assembler
Whole Genome Shotgun and EST Sequence Assembler
Mlv-smile
Find statistically significant patterns in sequences
Mothur
sequence analysis suite for research on microbiota
Mptp
single-locus species delimitation
Mrbayes
Bayesian Inference of Phylogeny
Mummer
Efficient sequence alignment of full genomes
Murasaki
homology detection tool across multiple large genomes
Muscle
Multiple alignment program of protein sequences
Mustang
multiple structural alignment of proteins
Nanopolish
consensus caller for nanopore sequencing data
Nast-ier
NAST-based DNA alignment tool
Ncbi-blast+
next generation suite of BLAST sequence search tools
Ncbi-blast+-legacy
NCBI Blast legacy call script
Ncbi-entrez-direct
NCBI Entrez utilities on the command line
Ncbi-epcr
Tool to test a DNA sequence for the presence of sequence tagged sites
Ncbi-seg
tool to mask segments of low compositional complexity in amino acid sequences
Ncbi-tools-bin
NCBI libraries for biology applications (text-based utilities)
Ncbi-tools-x11
NCBI libraries for biology applications (X-based utilities)
Ncl-tools
tools to deal with NEXUS files
Ncoils
coiled coil secondary structure prediction
Neobio
computes alignments of amino acid and nucleotide sequences
Njplot
phylogenetic tree drawing program
Norsnet
tool to identify unstructured loops in proteins
Norsp
predictor of non-regular secondary structure
Openms
package for LC/MS data management and analysis
Paleomix
pipelines and tools for the processing of ancient and modern HTS data
Paml
Phylogenetic Analysis by Maximum Likelihood (PAML)
Paraclu
Parametric clustering of genomic and transcriptomic features
Parsinsert
Parsimonious Insertion of unclassified sequences into phylogenetic trees
Parsnp
rapid core genome multi-alignment
Pbalign
map Pacific Biosciences reads to reference DNA sequences
Pbbarcode
annotate PacBio sequencing reads with barcode information
Pbdagcon
sequence consensus using directed acyclic graphs
Pbgenomicconsensus
Pacific Biosciences variant and consensus caller
Pbh5tools
tools for manipulating Pacific Biosciences HDF5 files
Pbhoney
genomic structural variation discovery
Pbjelly
genome assembly upgrading tool
Pbsim
simulator for PacBio sequencing reads
Pbsuite
software for Pacific Biosciences sequencing data
Pdb2pqr
Preparation of protein structures for electrostatics calculations
Perlprimer
Graphical design of primers for PCR
Perm
efficient mapping of short reads with periodic spaced seeds
Pftools
build and search protein and DNA generalized profiles
Phast
phylogenetic analysis with space/time models
Phipack
PHI test and other tests of recombination
Phybin
binning/clustering newick trees by topology
Phylip
package of programs for inferring phylogenies
Phyml
Phylogenetic estimation using Maximum Likelihood
Physamp
sample sequence alignment according to its corresponding phylogenetic tree
Phyutility
simple analyses or modifications on both phylogenetic trees and data matrices
Picard-tools
Command line tools to manipulate SAM and BAM files
Piler
genomic repeat analysis
Pirs
Profile based Illumina pair-end Reads Simulator
Placnet
Plasmid Constellation Network project
Plasmidomics
draw plasmids and vector maps with PostScript graphics export
Plast
Parallel Local Sequence Alignment Search Tool
Plink
whole-genome association analysis toolset
Plink1.9
whole-genome association analysis toolset
Plip
fully automated protein-ligand interaction profiler
Poa
Partial Order Alignment for multiple sequence alignment
Populations
population genetic software
Poretools
toolkit for nanopore nucleotide sequencing data
Prank
Probabilistic Alignment Kit for DNA, codon and amino-acid sequences
Predictnls
prediction and analysis of protein nuclear localization signals
Predictprotein
suite of protein sequence analysis tools
Prime-phylo
bayesian estimation of gene trees taking the species tree into account
Primer3
tool to design flanking oligo nucleotides for DNA amplification
Proalign
Probabilistic multiple alignment program
Probabel
Toolset for Genome-Wide Association Analysis
Probalign
multiple sequence alignment using partition function posterior probabilities
Probcons
PROBabilistic CONSistency-based multiple sequence alignment
Proda
multiple alignment of protein sequences
Prodigal
Microbial (bacterial and archaeal) gene finding program
Profbval
predictor of flexible/rigid protein residues from sequence
Profisis
prediction of protein-protein interaction sites from sequence
Profnet-bval
neural network architecture for profbval
Profnet-chop
neural network architecture for profchop
Profnet-con
neural network architecture for profcon
Profnet-isis
neural network architecture for profisis
Profnet-md
neural network architecture for metadisorder
Profnet-norsnet
neural network architecture for norsnet
Profnet-prof
neural network architecture for profacc
Profnet-snapfun
neural network architecture for snapfun
Profphd
secondary structure and solvent accessibility predictor
Profphd-net
neural network architecture for profphd
Profphd-utils
profphd helper utilities convert_seq and filter_hssp
Proftmb
per-residue prediction of bacterial transmembrane beta barrels
Progressivemauve
multiple genome alignment algorithms
Proteinortho
Detection of (Co-)orthologs in large-scale protein analysis
Prottest
selection of best-fit models of protein evolution
Psortb
bacterial localization prediction tool
Pycorrfit
tool for fitting correlation curves on a logarithmic plot
Pymol
Molecular Graphics System
Pynast
alignment of short DNA sequences
Pyscanfcs
scientific tool for perpendicular line scanning FCS
Python-cogent
framework for genomic biology
Python-treetime
inference of time stamped phylogenies and ancestral reconstruction
Python3-biomaj3
BioMAJ workflow management library
Qcumber
quality control of genomic sequences
Qiime
Quantitative Insights Into Microbial Ecology
Qtltools
Tool set for molecular QTL discovery and analysis
Quorum
QUality Optimized Reads of genomic sequences
R-bioc-annotate
BioConductor annotation for microarrays
R-bioc-biostrings
GNU R string objects representing biological sequences
R-bioc-cummerbund
tool for analysis of Cufflinks RNA-Seq output
R-bioc-deseq2
R package for RNA-Seq Differential Expression Analysis
R-bioc-dnacopy
R package: DNA copy number data analysis
R-bioc-ebseq
R package for RNA-Seq Differential Expression Analysis
R-bioc-genefilter
methods for filtering genes from microarray experiments
R-bioc-geneplotter
R package of functions for plotting genomic data
R-bioc-gviz
Plotting data and annotation information along genomic coordinates
R-bioc-hilbertvis
GNU R package to visualise long vector data
R-bioc-limma
linear models for microarray data
R-bioc-mergeomics
Integrative network analysis of omics data
R-bioc-metagenomeseq
GNU R statistical analysis for sparse high-throughput sequencing
R-bioc-phyloseq
GNU R handling and analysis of high-throughput microbiome census data
R-bioc-rtracklayer
GNU R interface to genome browsers and their annotation tracks
R-cran-adegenet
GNU R exploratory analysis of genetic and genomic data
R-cran-adephylo
GNU R exploratory analyses for the phylogenetic comparative method
R-cran-ape
GNU R package for Analyses of Phylogenetics and Evolution
R-cran-bio3d
GNU R package for biological structure analysis
R-cran-distory
GNU R distance between phylogenetic histories
R-cran-genabel
GNU R package for genome-wide SNP association analysis
R-cran-phangorn
GNU R package for phylogenetic analysis
R-cran-pscbs
R package: Analysis of Parent-Specific DNA Copy Numbers
R-cran-qtl
GNU R package for genetic marker linkage analysis
R-cran-rotl
GNU R interface to the 'Open Tree of Life' API
R-cran-seqinr
GNU R biological sequences retrieval and analysis
R-cran-treescape
GNU R Statistical Exploration of Landscapes of Phylogenetic Trees
R-cran-vegan
Community Ecology Package for R
R-other-mott-happy.hbrem
GNU R package for fine-mapping complex diseases
Radiant
explore hierarchical metagenomic data with zoomable pie charts
Rambo-k
Read Assignment Method Based On K-mers
Rapmap
rapid sensitive and accurate DNA read mapping via quasi-mapping
Rasmol
Visualize biological macromolecules
Raster3d
tools for generating images of proteins or other molecules
Rate4site
detector of conserved amino-acid sites
Raxml
Randomized Axelerated Maximum Likelihood of phylogenetic trees
Ray
de novo genome assemblies of next-gen sequencing data
Rdp-alignment
Ribosomal Database Project (RDP) alignment tools package
Rdp-classifier
extensible sequence classifier for fungal lsu, bacterial and archaeal 16s
Rdp-readseq
Ribosomal Database Project (RDP) sequence reading and writing
Readseq
Conversion between sequence formats
Reapr
universal tool for genome assembly evaluation
Relion-bin
toolkit for 3D reconstructions in cryo-electron microscopy
Relion-bin+gui
parallel toolkit for 3D reconstructions in cryo-electron microscopy
Relion-bin+mpi
parallel toolkit for 3D reconstructions in cryo-electron microscopy
Relion-bin+mpi+gui
parallel toolkit for 3D reconstructions in cryo-electron microscopy
Repeatmasker-recon
finds repeat families from biological sequences
Reprof
protein secondary structure and accessibility predictor
Rna-star
ultrafast universal RNA-seq aligner
Rnahybrid
Fast and effective prediction of microRNA/target duplexes
Roary
high speed stand alone pan genome pipeline
Roguenarok
versatile and scalable algorithm for rogue taxon identification
Rsem
RNA-Seq by Expectation-Maximization
Rtax
Classification of sequence reads of 16S ribosomal RNA gene
Runcircos-gui
GUI tool to run circos
Saint
Significance Analysis of INTeractome
Salmon
wicked-fast transcript quantification from RNA-seq data
Sambamba
tools for working with SAM/BAM data
Samtools
processing sequence alignments in SAM and BAM formats
Scrm
simulator of evolution of genetic sequences
Scythe
Bayesian adaptor trimmer for sequencing reads
Seaview
Multiplatform interface for sequence alignment and phylogeny
Seer
genomic sequence element (kmer) enrichment analysis
Seqan-apps
C++ library for the analysis of biological sequences
Seqprep
stripping adaptors and/or merging paired reads of DNA sequences with overlap
Seqsero
Salmonella serotyping from genome sequencing data
Seqtk
Fast and lightweight tool for processing sequences in the FASTA or FASTQ format
Sga
de novo genome assembler that uses string graphs
Sibsim4
align expressed RNA sequences on a DNA template
Sickle
windowed adaptive trimming tool for FASTQ files using quality
Sigma-align
Simple greedy multiple alignment of non-coding DNA sequences
Sim4
tool for aligning cDNA and genomic DNA
Sim4db
batch spliced alignment of cDNA sequences to a target genome
Smalt
Sequence Mapping and Alignment Tool
Smithwaterman
determine similar regions between two strings or genomic sequences
Smrtanalysis
software suite for single molecule, real-time sequencing
Snap
location of genes from DNA sequence with hidden markov model
Snap-aligner
Scalable Nucleotide Alignment Program
Sniffles
structural variation caller using third-generation sequencing
Snp-sites
Binary code for the package snp-sites
Snpomatic
fast, stringent short-read mapping software
Soapdenovo
short-read assembly method to build de novo draft assembly
Soapdenovo2
short-read assembly method to build de novo draft assembly
Sortmerna
tool for filtering, mapping and OTU-picking NGS reads
Spaced
alignment-free sequence comparison using spaced words
Spades
genome assembler for single-cell and isolates data sets
Sprai
single-pass sequencing read accuracy improver
Spread-phy
analyze and visualize phylogeographic reconstructions
Squizz
Converter for genetic sequences and alignments
Sra-toolkit
utilities for the NCBI Sequence Read Archive
Srst2
Short Read Sequence Typing for Bacterial Pathogens
Ssake
genomics application for assembling millions of very short DNA sequences
Sspace
scaffolding pre-assembled contigs after extension
Ssw-align
Smith-Waterman aligner based on libssw
Stacks
pipeline for building loci from short-read DNA sequences
Staden
DNA sequence assembly (Gap4/Gap5), editing and analysis tools
Staden-io-lib-utils
programs for maniuplating DNA sequencing files
Subread
toolkit for processing next-gen sequencing data
Suitename
categorize each suite in an RNA backbone
Sumaclust
fast and exact clustering of genomic sequences
Sumatra
fast and exact comparison and clustering of sequences
Sumtrees
Phylogenetic Tree Summarization and Annotation
Surankco
Supervised Ranking of Contigs in de novo Assemblies
Swarm
robust and fast clustering method for amplicon-based studies
T-coffee
Multiple Sequence Alignment
Tabix
generic indexer for TAB-delimited genome position files
Tantan
low complexity and tandem repeat masker for biosequences
Theseus
superimpose macromolecules using maximum likelihood
Tigr-glimmer
Gene detection in archea and bacteria
Tm-align
structural alignment of proteins
Tnseq-transit
statistical calculations of essentiality of genes or genomic regions
Tophat
fast splice junction mapper for RNA-Seq reads
Topp
set of programs implementing The OpenMS Proteomic Pipeline
Toppred
transmembrane topology prediction
Transdecoder
find coding regions within RNA transcript sequences
Transrate-tools
helper for transrate
Transtermhp
find rho-independent transcription terminators in bacterial genomes
Tree-ppuzzle
Parallelized reconstruction of phylogenetic trees by maximum likelihood
Tree-puzzle
Reconstruction of phylogenetic trees by maximum likelihood
Treeview
Java re-implementation of Michael Eisen's TreeView
Treeviewx
Displays and prints phylogenetic trees
Trimmomatic
flexible read trimming tool for Illumina NGS data
Trinityrnaseq
RNA-Seq De novo Assembly
Uc-echo
error correction algorithm designed for short-reads from NGS
Varna
Visualization Applet for RNA
Vcftools
Collection of tools to work with VCF files
Velvet
Nucleic acid sequence assembler for very short reads
Velvet-long
Nucleic acid sequence assembler for very short reads, long version
Velvetoptimiser
automatically optimise Velvet do novo assembly parameters
Vsearch
tool for processing metagenomic sequences
Wigeon
reimplementation of the Pintail 16S DNA anomaly detection utility
Wise
comparison of biopolymers, like DNA and protein sequences
Zalign
parallel local alignment of biological sequences

Official Debian packages with lower relevance

Adun.app
Molecular Simulator for GNUstep (GUI)
Biomaj
biological data-bank updater
Cain
simulations of chemical reactions
Dascrubber
alignment-based scrubbing pipeline for DNA sequencing reads
Emboss-explorer
web-based GUI to EMBOSS
Getdata
management of external databases
Maude
high-performance logical framework
Melting-gui
graphical interface to compute the melting temperature of nucleic acid duplex
Metastudent-data
predictor of Gene Ontology terms from protein sequence - data files
Metastudent-data-2
predictor of Gene Ontology terms from protein sequence - data #2
Mobyle
Web portal that provides web forms for command-line software
Mobyle-programs
Program descriptions for the mobyle portal
Mobyle-tutorials
program tutorials for the mobyle portal
Mrs
Information Retrieval System for Biomedical databanks
R-bioc-annotationhub
GNU R client to access AnnotationHub resources
R-bioc-aroma.light
BioConductor methods normalization and visualization of microarray data
R-bioc-ensembldb
GNU R utilities to create and use an Ensembl based annotation database
R-bioc-go.db
annotation maps describing the entire Gene Ontology
R-bioc-savr
GNU R parse and analyze Illumina SAV files
R-cran-boolnet
assembling, analyzing and visualizing Boolean networks
R-cran-pheatmap
GNU R package to create pretty heatmaps
R-cran-qqman
R package for visualizing GWAS results using Q-Q and manhattan plots
R-cran-rentrez
GNU R interface to the NCBI's EUtils API
Science-workflow
workflow management systems useful for scientific research

Debian packages in contrib or non-free

Arb
phylogenetic sequence analysis suite - main program
Autodocktools
GUI to help set up, launch and analyze AutoDock dockings
Biomaj-watcher
biological data-bank updater - web interface
Blimps-utils
blocks database improved searcher
Cluster3
Reimplementation of the Eisen-clustering software
Cufflinks
Transcript assembly, differential expression and regulation for RNA-Seq
Embassy-phylip
EMBOSS conversions of the programs in the phylip package
Gmap
spliced and SNP-tolerant alignment for mRNA and short reads
Igv
Integrative Genomics Viewer
Mgltools-cadd
Computer Aided Drug Discovery (CADD) Pipeline
Mgltools-pmv
Python-based Molecular Viewer
Mgltools-vision
Python-based Visual Programming Environment
Raccoon
preparation of in silico drug screening projects
Seq-gen
simulate the evolution of nucleotide or amino acid sequences
Sift
predicts if a substitution in a protein has a phenotypic effect
Trnascan-se
detection of transfer RNA genes in genomic sequence
Ugene
integrated bioinformatics toolkit
Varscan
variant detection in next-generation sequencing data

Debian packages in experimental

Tvc
genetic variant caller for Ion Torrent sequencing platforms

Debian packages in New queue (hopefully available soon)

Hinge
long read genome assembler based on hinging
Nanook
pre- and post-alignment analysis of nanopore sequencing data

Packaging has started and developers might try the packaging code in VCS

Acacia
Error-corrector for pyrosequenced amplicon reads.
Amos-assembler
modular whole genome assembler
Apollo
genome annotation viewer and editor
Axparafit
optimized statistical analysis of host-parasite coevolution
Axpcoords
highly optimized and parallelized porting of pcoords
Bagpipe
genomewide LD mapping
Bandage
Bioinformatics Application for Navigating De novo Assembly Graphs Easily
Biceps
error-tolerant peptide identification
Bigsdb
Bacterial Isolate Genome Sequence Database
Bitseq
Bayesian Inference of Transcripts from Sequencing Data
Blat
BLAST-Like Alignment Tool
Blixem
interactive browser of sequence alignments
Blobology
tool set for the visualisation of genome assemblies
Card-rgi
analysis of genome sequences using the Resistance Gene Identifier
Cinema
multi-sequence alignment editor and viewer
Clonalframeml
Efficient Inference of Recombination in Whole Bacterial Genomes
Clonalorigin
inference of homologous recombination in bacteria using whole genome sequences
Cnvkit
Copy number variant detection from targeted DNA sequencing
Condetri
straight-forward trimming of FASTQ sequences
Contrafold
CONditional TRAining for RNA Secondary Structure Prediction
Coot
model building program for macromolecular crystallography
Crossbow
Genotyping from short reads using cloud computing
Crux-toolkit
toolkit for tandem mass spectrometry analysis
Cytoscape
visualizing molecular interaction networks
Dazzle
Java-based DAS server
Ecell
Concept and environment for constructing virtual cells on computers
Emmax
genetic mapping considering population structure
Ensembl
basic Ensembl genome browser
Euler-sr
correcting errors in short gene sequence reads and assembling them
Euler2
de novo repeat classification and fragment assembly
Exabayes
bayesian phylogenetic tree inference for large-scale analyses
Fasta3
tools for searching collections of biological sequences
Ffp
Feature Frequency Profile Phylogeny
Forester
Graphical vizualiation tool Archaeopteryx
Galaxy
XXX
Gassst
Global alignment short sequence search tool
Gatb-core
The Genome Analysis Toolbox with de-Bruijn graph
Gatk
The Genome Analysis Toolkit
Grabix
wee tool for random access into BGZF files
Grogui
graphical user interface for popular molecular dynamics package GROMACS
Haploview
Analysis and visualization of LD and haplotype maps
Hawkeye
Interactive Visual Analytics Tool for Genome Assemblies
Htqc
Quality control and filtration for illumina sequencing data
Inspect
mass-spectrometry database search tool
Jbrowse
The JBrowse Genome Browser
Kclust
clustering of protein sequences
Kempbasu
Significance tests for comparing digital gene expression profiles
Lagan
highly parametrizable pairwise global alignment program
Lofreq
sensitive variant calling from sequencing data
Logomat-m
visualize central aspects of Profile Hidden Markov Models (pHMMs)
Mach-haplotyper
Markov Chain based SNP haplotyper
Mage2tab
MAGE-MLv1 converter and visualiser
Malt
MEGAN alignment tool
Manta
structural variant and indel caller for mapped sequencing data
Martj
distributed data integration system for biological data
Meme
search for common motifs in DNA or protein sequences
Mesquite
modular system for evolutionary analysis
Metabit
analysing microbial profiles from high-throughput sequencing shotgun data
Modeller
Protein structure modeling by satisfaction of spatial restraints
Molekel
Advanced Interactive 3D-Graphics for Molecular Sciences
Mosaik-aligner
reference-guided aligner for next-generation sequencing
Mpsqed
alignment editor and multiplex pyrosequencing assay designer
Mugsy
multiple whole genome alignment tool
Nanocall
Basecaller for Oxford Nanopore Sequencing Data
Nextsv
automated structural variation detection for long-read sequencing
Ngila
global pairwise alignments with logarithmic and affine gap costs
Ngsqctoolkit
toolkit for the quality control of next generation sequencing data
Nw-align
global protein sequence alignment
Oases
de novo transcriptome assembler for very short reads
Obitools
programs to analyze NGS data in a DNA metabarcoding context
Pal2nal
converts proteins to genomic DNA alignment
Partitionfinder
choses partitioning schemes and models of molecular evolution for sequence data
Patman
rapid alignment of short sequences to large databases
Patristic
Calculate patristic distances and comparing the components of genetic change
Pcma
fast and accurate multiple sequence alignment based on profile consistency
Phylophlan
microbial Tree of Life using 400 universal proteins
Phyloviz-core
phylogenetic inference and data visualization for sequence based typing methods
Pipasic
Protein Abundance Correction in Metaproteomic Data
Plato
Analysis, translation, and organization of large-scale genetic data
Profit
Protein structure alignment
Prokka
rapid annotation of prokaryotic genomes
Pscan-tfbs
search for transcription factor binding sites
Psipred
protein secondary structure prediction
Pssh2
set of scripts for mapping protein sequence to structure
Python-reaper
QTL analysis for expression data
Qualimap
evaluating next generation sequencing alignment data
R-cran-metamix
GNU R bayesian mixture analysis for metagenomic community profiling
R-other-apmswapp
GNU R Pre- and Postprocessing For Affinity Purification Mass Spectrometry
R-other-valdar-bagphenotype.library
GNU R extension of the functionality of happy
Raxml-ng
phylogenetic tree inference tool which uses maximum-likelihood
Repeatmasker
screen DNA sequences for interspersed repeats
Roadtrips
case-control association testing with unknown population and pedigree structure
Rosetta
molecular biophysics for structural biology
Rsat
Regulatory Sequence Analysis Tools
Sap
Pairwise protein structure alignment via double dynamic programming
Scoary
pangenome-wide association studies
Segemehl
short read mapping with gaps
Sequenceconverter.app
biological sequence file format conversion applet for GNUstep
Sistr
Salmonella In Silico Typing Resource (SISTR)
Situs
Modeling of atomic resolution structures into low-resolution density maps
Snpeff
genetic variant annotation and effect prediction toolbox
Sparta
automated reference-based bacterial RNA-seq Transcriptome Analysis
Ssaha
Sequence Search and Alignment by Hashing Algorithm
Strap
Comfortable and intuitive protein alignment editor / viewer
Strap-base
essential files for the interactive alignment viewer and editor Strap
Tacg
command line program for finding patterns in nucleic acids
Tide
SEQUEST Searching for Peptide Identification from Tandem Mass Spectra
Tigr-glimmer-mg
finding genes in environmental shotgun DNA sequences
Tn-seqexplorer
explore and analyze Tn-seq data for prokaryotic genomes
Umap
quantify genome and methylome mappability
Unc-fish
Fast Identification of Segmental Homology
Varmatch
robust matching of small genomic variant datasets
Vienna-rna
RNA sequence analysis
Vmd
presentation of traces of molecular dynamics runs
Zodiac-zeden
ZODIAC - Zeden's Organise DIsplay And Compute

Unofficial packages built by somebody else

Big-blast
Helper tool to run blast on large sequences
Caftools
Tools to maintain DNA sequence assemblies
Cap3
DNA Sequence Assembly Program
Coalesce
outdated program to estimate population-genetic parameters
Compclust
explore and quantify relationships between clustering results
Estferret
processes, clusters and annotates EST data
Estscan
detect coding regions in DNA sequences, even if of low quality
Fasta
searching DNA and protein databases
Fluctuate
outdated program to model a single population
Lamarc
estimate population-genetic parameters
Lucy
DNA sequence quality and vector trimming tool
Maxd
data warehouse and visualisation environment for genomic expression data
Migrate
estimation of population sizes and gene flow using the coalescent
Msatfinder
identification and characterization of microsatellites in a comparative genomic context
Mview
reformat results of a sequence database search or a multiple alignment
Oligoarrayaux
Prediction of Melting Profiles for Nucleic Acids
Omegamap
detecting natural selection and recombination in DNA or RNA sequences
Partigene
generating partial gemomes
Pfaat
Protein Family Alignment Annotation Tool
Pftools
tools to handle profiles of protein domains from PROSITE
Prot4est
EST protein translation suite
Python-orange
Data mining framework
Qtlcart
map quantitative traits using a map of molecular markers
Rbs-finder
find ribosome binding sites(RBS)
Recombine
effective population size of populations
Roche454ace2caf
convert GS20 or FLX assemblies into CAF format
Splitstree
Analyzing and Visualizing Evolutionary Data
Taverna
designing and executing myGrid workflows for bioinformatics
Taxinspector
browser for entries in the NCBI taxonomy
Tetra
tetranucleotide frequency calculator
Trace2dbest
process trace files into dbEST submissions

No known packages available but some record of interest (WNPP bug)

Btk-core
biomolecule Toolkit C++ library
Mirbase
The microRNA sequence database
Phylowin
Graphical interface for molecular phylogenetic inference

No known packages available

Amoscmp
comparative genome assembly package
Annovar
annotate genetic variants detected from diverse genomes
Arachne
toolkit for Whole Genome Shotgun Assembly
Asap
organize the data associated with a genome
Bambus
hierarchical approach to building contig scaffolds
Cactus
Cdna-db
quality-control checking of finished cDNA clone sequences
Cmap
view comparisons of genetic and physical maps
Contralign
parameter learning framework for protein pairwise sequence alignment
Copycat
fast access to cophylogenetic analyses
Das-proserver
lightweight Distributed Annotation System (DAS) server
Decipher
tracks duplications and deletions of DNA in patients
E-hive
distributed processing system based on 'autonomous agents'
Elph
motif finder that can find ribosome binding sites, exon splicing enhancers, or regulatory sites
Est-db
Software suite for expressed sequence tag (EST) sequencing
Exalt
phylogenetic generalized hidden Markov model for predicting alternatively spliced exons
Excavator
gene expression data clustering
Figaro
novel vector trimming software
Finex
sequence homology searching
Forge
genome assembler for mixed read types
Gbioseq
DNA sequence editor for Linux
Gbrowse-syn
Generic Synteny Browser
Genemark
family of gene prediction programs
Genesplicer
computational method for splice site prediction
Genetrack
genomic data storage and visualization framework
Genezilla
eukaryotic gene finder
Genographer
read data and reconstruct them into a gel image
Glimmerhmm
Eukaryotic Gene-Finding System
Gmv
comparative genome browser for Murasaki
Hexamer
scan DNA sequences to look for likely coding regions
Hilbertvisgui
interactive tool to visualize long vectors of integer data by means of Hilbert curves
Jigsaw
gene prediction using multiple sources of evidence
Jstreeview
Editor for Phylogenetic Trees
Maker2
annotate genomes and create genome databases
Metarep
JCVI Metagenomics Reports
Minimus
AMOS lightweight assembler
Mummergpu
High-throughput sequence alignment using Graphics Processing Units
Obo-edit
editor for biological ontologies
Operondb
detect and analyze conserved gene pairs
Phagefinder
heuristic computer program to identify prophage regions within bacterial genomes
Phpphylotree
draw phylogenetic trees
Phylographer
Graph Visualization Tool
Pyrophosphate-tools
for assembling and searching pyrophosphate sequence data
Rmblast
RepeatMasker compatible version of the standard NCBI BLAST
Rose
Region-Of-Synteny Extractor
Spice
Distributed Annotation System (DAS) client
Tracetuner
DNA sequencing and trace processing
Treebuilder3d
viewer of SAGE and other types of gene expression data
Treetime
Bayesian sampling of phylogenetic trees from molecular data
Tripal
collection of Drupal modules for genomic research
Twain
syntenic genefinder employing a Generalized Pair Hidden Markov Model
Uniprime
workflow-based platform for universal primer design
X-tandem-pipeline
peptide/protein identification from MS/MS mass spectra

Biology development - Debian Med packages for development of bioinformatics applications

This metapackage will install Debian packages which might be helpful for development of applications for biological research.

Official Debian packages with high relevance

Bio-tradis
analyse the output from TraDIS analyses of genomic sequences
Bioperl
Perl tools for computational molecular biology
Bioperl-run
BioPerl wrappers: scripts
Biosquid
utilities for biological sequence analysis
Libace-perl
Object-Oriented Access to ACEDB Databases
Libai-fann-perl
Perl wrapper for the FANN library
Libbambamc-dev
Development files for reading and writing BAM (genome alignment) files
Libbamtools-dev
C++ API for manipulating BAM (genome alignment) files
Libbio-coordinate-perl
BioPerl modules for working with biological coordinates
Libbio-das-lite-perl
implementation of the BioDas protocol
Libbio-eutilities-perl
BioPerl interface to the Entrez Programming Utilities (E-utilities)
Libbio-graphics-perl
Generate GD images of Bio::Seq objects
Libbio-mage-perl
Container module for classes in the MAGE package: MAGE
Libbio-mage-utils-perl
Extra modules for classes in the MAGE package: MAGE
Libbio-primerdesigner-perl
Perl module to design PCR primers using primer3 and epcr
Libbiococoa-dev
Bioinformatics framework for GNUstep and Cocoa (development files)
Libbiod-dev
bioinformatics library in D (development files)
Libbiojava-java
Java API to biological data and applications (default version)
Libbiojava4-java
Java API to biological data and applications (default version)
Libblasr-dev
tools for aligning PacBio reads to target sequences (development files)
Libbpp-core-dev
Bio++ Core library development files
Libbpp-phyl-dev
Bio++ Phylogenetic library development files
Libbpp-phyl-omics-dev
Bio++ Phylogenetics library: genomics components (development files)
Libbpp-popgen-dev
Bio++ Population Genetics library development files
Libbpp-qt-dev
Bio++ Qt Graphic classes library development files
Libbpp-raa-dev
Bio++ Remote Acnuc Access library development files
Libbpp-seq-dev
Bio++ Sequence library development files
Libbpp-seq-omics-dev
Bio++ Sequence library: genomics components (development files)
Libchado-perl
database schema and tools for genomic data
Libconsensuscore-dev
algorithms for PacBio multiple sequence consensus -- development files
Libdivsufsort-dev
libdivsufsort header files
Libfast5-dev
library for reading Oxford Nanopore Fast5 files -- headers
Libfastahack-dev
library for indexing and sequence extraction from FASTA files (devel)
Libffindex0-dev
library for simple index/database for huge amounts of small files (development)
Libfml-dev
development headers for libfml
Libfreecontact-dev
fast protein contact predictor library - development files
Libfreecontact-perl
fast protein contact predictor - binding for Perl
Libgenome-1.3-dev
toolkit for developing bioinformatic related software (devel)
Libgenome-model-tools-music-perl
module for finding mutations of significance in cancer
Libgenome-perl
pipelines, tools, and data management for genomics
Libgenometools0-dev
development files for GenomeTools
Libgff-dev
GFF/GTF parsing from cufflinks as a library
Libgkarrays-dev
library to query large collection of NGS sequences (development)
Libgo-perl
perl modules for GO and other OBO ontologies
Libhmsbeagle-dev
High-performance lib for Bayesian and Maximum Likelihood phylogenetics (devel)
Libhts-dev
Development files for the HTSlib
Libhtsjdk-java
Java API for high-throughput sequencing data (HTS) formats
Libjebl2-java
Java Evolutionary Biology Library
Libjloda-java
Java library of data structures and algorithms for bioinformatics
Libkmer-dev
suite of tools for DNA sequence analysis (development lib)
Libmems-1.6-dev
development library to support DNA string matching and comparative genomics
Libminimap-dev
development headers for libminimap
Libmuscle-3.7-dev
multiple alignment development library for protein sequences
Libncbi-vdb-dev
libraries for using data in the INSDC Sequence Read Archives (devel)
Libncbi6-dev
NCBI libraries for biology applications (development files)
Libncl-dev
NEXUS Class Library (static lib and header files)
Libngs-java
Next Generation Sequencing language Bindings (Java bindings)
Libngs-sdk-dev
Next Generation Sequencing language Bindings (development)
Libnhgri-blastall-perl
Perl extension for running and parsing NCBI's BLAST 2.x
Libopenms-dev
library for LC/MS data management and analysis - dev files
Libpal-java
Phylogenetic Analysis Library
Libpbbam-dev
Pacific Biosciences binary alignment/map (BAM) library (headers)
Libpbdata-dev
tools for handling PacBio sequences (development files)
Libpbihdf-dev
tools for handling PacBio hdf5 files (development files)
Libpbseq-dev
library for analyzing PacBio sequencing data (development files)
Libqes-dev
DNA sequence parsing library -- development
Librcsb-core-wrapper0-dev
development files for librcsb-core-wrapper0
Librdp-taxonomy-tree-java
taxonomy tree library from Ribosomal Database Project (RDP)
Librelion-dev
C++ API for RELION (3D reconstructions in cryo-electron microscopy)
Librg-blast-parser-perl
very fast NCBI BLAST parser - binding for Perl
Librg-reprof-bundle-perl
protein secondary structure and accessibility predictor (perl module)
Librostlab-blast0-dev
very fast C++ library for parsing the output of NCBI BLAST programs (devel)
Librostlab3-dev
C++ library for computational biology (development)
Libsbml5-dev
System Biology Markup Language library - development files
Libseqlib-dev
C++ htslib/bwa-mem/fermi interface for interrogating sequence data (dev)
Libsmithwaterman-dev
determine similar regions between two strings or genomic sequences (devel)
Libsnp-sites1-dev
Static libraries and header files for the package snp-sites
Libsort-key-top-perl
Perl module to select and sort top n elements of a list
Libsrf-dev
C++ implementation of the SRF format for DNA sequence data
Libssm-dev
macromolecular superposition library - development files
Libssw-dev
Development headers and static libraries for libssw
Libssw-java
Java bindings for libssw
Libstaden-read-dev
development files for libstaden-read
Libswiss-perl
Perl API to the UniProt database
Libtabixpp-dev
C++ wrapper to tabix indexer (development files)
Libtfbs-perl
scanning DNA sequence with a position weight matrix
Libvcflib-dev
C++ library for parsing and manipulating VCF files (development)
Libvibrant6-dev
NCBI libraries for graphic biology applications (development files)
Libzerg-perl
fast perl module for parsing the output of NCBI BLAST programs
Libzerg0-dev
development libraries and header files for libzerg
Mcl
Markov Cluster algorithm
Octave-bioinfo
bioinformatic functions for Octave
Pyfai
Fast Azimuthal Integration scripts
Python-biom-format
Biological Observation Matrix (BIOM) format (Python 2)
Python-biopython
Python library for bioinformatics (implemented in Python 2)
Python-biotools
Python bioinformatics utilities for high-throughput genomic sequencing
Python-cobra
constraint-based modeling of biological networks (Python 2)
Python-cogent
framework for genomic biology
Python-corepywrap
library that exports C++ mmCIF accessors to Python
Python-csb
Python framework for structural bioinformatics
Python-cutadapt
Clean biological sequences from high-throughput sequencing reads (Python 2)
Python-dendropy
DendroPy Phylogenetic Computing Library (Python 2)
Python-fast5
library for reading Oxford Nanopore Fast5 files -- Python 2
Python-freecontact
fast protein contact predictor - binding for Python
Python-htseq
high-throughput genome sequencing read analysis utilities
Python-intervaltree-bio
Interval tree convenience classes for genomic data -- Python 2 library
Python-kineticstools
detection of DNA modifications (Python 2 library)
Python-mmtk
molecular modeling toolkit
Python-ngs
Next Generation Sequencing language Bindings (Python bindings)
Python-pbcommand
common command-line interface for Pacific Biosciences analysis modules
Python-pbconsensuscore
algorithms for PacBio multiple sequence consensus -- Python 2
Python-pbcore
Python library for processing PacBio data files
Python-pbh5tools
tools for manipulating Pacific Biosciences HDF5 files -- Python 2 library
Python-pyfaidx
efficient random access to fasta subsequences for Python
Python-pysam
interface for the SAM/BAM sequence alignment and mapping format (Python 2)
Python-pyvcf
Variant Call Format (VCF) parser for Python
Python-rdkit
Collection of cheminformatics and machine-learning software
Python-ruffus
Python computation pipeline library widely used in bioinformatics
Python-screed
short nucleotide read sequence utils in Python 2
Python3-biomaj3
BioMAJ workflow management library
Python3-biopython
Python library for bioinformatics (implemented in Python 3)
Python3-biotools
Python3 bioinformatics utilities for high-throughput genomic sequencing
Python3-csb
Python framework for structural bioinformatics (Python3 version)
Python3-cutadapt
Clean biological sequences from high-throughput sequencing reads (Python 3)
Python3-dendropy
DendroPy Phylogenetic Computing Library (Python 3)
Python3-fast5
library for reading Oxford Nanopore Fast5 files -- Python 3
Python3-gfapy
flexible and extensible software library for handling sequence graphs
Python3-gffutils
Work with GFF and GTF files in a flexible database framework
Python3-intervaltree-bio
Interval tree convenience classes for genomic data -- Python 3 library
Python3-ngs
Next Generation Sequencing language Bindings (Python3 bindings)
Python3-pbconsensuscore
algorithms for PacBio multiple sequence consensus -- Python 3
Python3-pybedtools
Python 3 wrapper around BEDTools for bioinformatics work
Python3-pyfaidx
efficient random access to fasta subsequences for Python 3
Python3-pymummer
Python 3 interface to MUMmer
Python3-pyvcf
Variant Call Format (VCF) parser for Python 3
Python3-ruffus
Python3 computation pipeline library widely used in bioinformatics
Python3-skbio
Python3 data structures, algorithms, educational resources for bioinformatic
R-bioc-biobase
base functions for Bioconductor
R-cran-genetics
GNU R package for population genetics
R-cran-haplo.stats
GNU R package for haplotype analysis
R-cran-phylobase
GNU R base package for phylogenetic structures and comparative data
R-cran-rncl
GNU R interface to the Nexus Class Library
R-cran-rnexml
GNU R package for semantically rich I/O for the 'NeXML' format
Ruby-bio
Ruby tools for computational molecular biology
Ruby-crb-blast
Run conditional reciprocal best blast
Sbmltoolbox
libsbml toolbox for octave and matlab
Seqan-dev
C++ library for the analysis of biological sequences (development)

Official Debian packages with lower relevance

Libbam-dev
manipulates nucleotide sequence alignments in BAM or SAM format
Libdisorder-dev
library for entropy measurement of byte streams (devel)
Libfreecontact-doc
documentation for libfreecontact
Libgtextutils-dev
Gordon Text_utils library (development files)
Libpbcopper-dev
data structures, algorithms, and utilities for C++ applications -- header files
Librostlab-blast-doc
very fast C++ library for parsing the output of NCBI BLAST programs (doc)
Librostlab-doc
C++ library for computational biology (documentation)
Python-biopython-doc
Documentation for the Biopython library
Python-biopython-sql
Biopython support for the BioSQL database schema (Python 2)
Python-pyflow
lightweight parallel task engine for Python
Python3-biopython-sql
Biopython support for the BioSQL database schema (Python 3)
R-bioc-affy
BioConductor methods for Affymetrix Oligonucleotide Arrays
R-bioc-affyio
BioConductor tools for parsing Affymetrix data files
R-bioc-altcdfenvs
BioConductor alternative CDF environments
R-bioc-annotationdbi
GNU R Annotation Database Interface for BioConductor
R-bioc-biocgenerics
generic functions for Bioconductor
R-bioc-biomart
GNU R Interface to BioMart databases (Ensembl, COSMIC, Wormbase and Gramene)
R-bioc-biomformat
GNU R interface package for the BIOM file format
R-bioc-biovizbase
GNU R basic graphic utilities for visualization of genomic data
R-bioc-bsgenome
BioConductor infrastructure for Biostrings-based genome data packages
R-bioc-genomeinfodb
BioConductor utilities for manipulating chromosome identifiers
R-bioc-genomicalignments
BioConductor representation and manipulation of short genomic alignments
R-bioc-genomicfeatures
GNU R tools for making and manipulating transcript centric annotations
R-bioc-genomicranges
BioConductor representation and manipulation of genomic intervals
R-bioc-graph
handle graph data structures for BioConductor
R-bioc-hypergraph
BioConductor hypergraph data structures
R-bioc-iranges
GNU R low-level containers for storing sets of integer ranges
R-bioc-makecdfenv
BioConductor CDF Environment Maker
R-bioc-preprocesscore
BioConductor collection of pre-processing functions
R-bioc-rbgl
R interface to the graph algorithms contained in the BOOST library
R-bioc-rsamtools
GNU R binary alignment (BAM), variant call (BCF), or tabix file import
R-bioc-shortread
GNU R classes and methods for high-throughput short-read sequencing data
R-bioc-snpstats
BioConductor SnpMatrix and XSnpMatrix classes and methods
R-bioc-variantannotation
BioConductor annotation of genetic variants
R-bioc-xvector
BioConductor representation and manpulation of external sequences
R-cran-natserv
GNU R 'NatureServe' Interface
R-cran-rentrez
GNU R interface to the NCBI's EUtils API
R-cran-rocr
GNU R package to prepare and display ROC curves
Ruby-rgfa
parse, edit and write GFA format graphs in Ruby

Debian packages in contrib or non-free

Mgltools-networkeditor
Python GUI library for the editing of networks
Mgltools-pybabel
molecular structure file access and interpretation
Mgltools-vision
Python-based Visual Programming Environment

Packaging has started and developers might try the packaging code in VCS

Gatb-core
The Genome Analysis Toolbox with de-Bruijn graph
Libforester-java
Libraries for evolutionary biology and comparative genomics research
Libqcpp-dev
C++11 library for NGS data quality control -- headers
Libroadrunner-dev
simulation engine for systems and synthetic biology (development)
Libswarm2-dev
agent-based modeling to education, biomedical research and others
Python-bd2k
utilities for BD2KGenomics (Python 2)
Python-biomaj3
biological data-bank updater (Python 2)
Python-bx
library to manage genomic data and its aligment
Python-consensuscore2
generate consensus sequences for PacBio data -- Python 2
Python-ete3
Python Environment for (phylogenetic) Tree Exploration - Python 2.X
Python-misopy
Mixture of Isoforms model for RNA-Seq isoform quantitation
Python-pyfasta
fast, memory-efficient Python 2 access to fasta sequence files
Python-roadrunner
Python bindings for libroadrunner
Python3-bx
library to manage genomic data and its alignment
Python3-consensuscore2
generate consensus sequences for PacBio data -- Python 3
Python3-ete3
Python Environment for (phylogenetic) Tree Exploration - Python 3.X
Python3-misopy
Mixture of Isoforms model for RNA-Seq isoform quantitation (Python 3)
Python3-pyfasta
fast, memory-efficient Python 3 access to fasta sequence files

No known packages available but some record of interest (WNPP bug)

Libgff-perl
Perl bindings for GFF Annotation Protocol

No known packages available

Bioclipse
platform for chemo- and bioinformatics based on Eclipse
Octace-bioinfo
Bioinformatics manipulation for Octave

Next generation sequencing - Debian Med bioinformatics applications usable in Next Generation Sequencing

It aims at gettting packages which specialize in the processing or interpretation of data generated with next- (and later-) generation high-thoughput sequencing technologies.

Official Debian packages with high relevance

Bcftools
genomic variant calling and manipulation of VCF/BCF files
Bedtools
suite of utilities for comparing genomic features
Blasr
mapping single-molecule sequencing reads
Bowtie
Ultrafast memory-efficient short read aligner
Bwa
Burrows-Wheeler Aligner
Daligner
local alignment discovery between long nucleotide sequencing reads
Fastx-toolkit
FASTQ/A short nucleotide reads pre-processing tools
Last-align
genome-scale comparison of biological sequences
Libvcflib-tools
C++ library for parsing and manipulating VCF files (tools)
Maq
maps short fixed-length polymorphic DNA sequence reads to reference sequences
Mhap
locality-sensitive hashing to detect long-read overlaps
Picard-tools
Command line tools to manipulate SAM and BAM files
R-bioc-hilbertvis
GNU R package to visualise long vector data
Rna-star
ultrafast universal RNA-seq aligner
Samtools
processing sequence alignments in SAM and BAM formats
Sra-toolkit
utilities for the NCBI Sequence Read Archive
Ssake
genomics application for assembling millions of very short DNA sequences
Tabix
generic indexer for TAB-delimited genome position files
Tophat
fast splice junction mapper for RNA-Seq reads
Vcftools
Collection of tools to work with VCF files
Velvet
Nucleic acid sequence assembler for very short reads

Phylogeny - Debian Med phylogeny packages

This lists Debian packages related to phylogeny for use in life sciences. The purpose of this compilation of packages is to have a handy subset of from the med-bio metapackage which contains a lot more than only phylogeny related software.

Official Debian packages with high relevance

Altree
program to perform phylogeny-based association and localization analysis
Beast-mcmc
Bayesian MCMC phylogenetic inference
Clustalw
global multiple nucleotide or peptide sequence alignment
Clustalx
Multiple alignment of nucleic acid and protein sequences (graphical interface)
Dialign
Segment-based multiple sequence alignment
Dialign-tx
Segment-based multiple sequence alignment
Exonerate
generic tool for pairwise sequence comparison
Fastdnaml
Tool for construction of phylogenetic trees of DNA sequences
Figtree
graphical phylogenetic tree viewer
Hmmer
profile hidden Markov models for protein sequence analysis
Iqtree
efficient phylogenetic software by maximum likelihood
Jmodeltest
HPC selection of models of nucleotide substitution
Kalign
Global and progressive multiple sequence alignment
Mrbayes
Bayesian Inference of Phylogeny
Muscle
Multiple alignment program of protein sequences
Mustang
multiple structural alignment of proteins
Njplot
phylogenetic tree drawing program
Phylip
package of programs for inferring phylogenies
Phyml
Phylogenetic estimation using Maximum Likelihood
Poa
Partial Order Alignment for multiple sequence alignment
Populations
population genetic software
Proalign
Probabilistic multiple alignment program
Probalign
multiple sequence alignment using partition function posterior probabilities
Probcons
PROBabilistic CONSistency-based multiple sequence alignment
Proda
multiple alignment of protein sequences
Prottest
selection of best-fit models of protein evolution
Seaview
Multiplatform interface for sequence alignment and phylogeny
Sigma-align
Simple greedy multiple alignment of non-coding DNA sequences
Spread-phy
analyze and visualize phylogeographic reconstructions
T-coffee
Multiple Sequence Alignment
Tm-align
structural alignment of proteins
Tree-ppuzzle
Parallelized reconstruction of phylogenetic trees by maximum likelihood
Tree-puzzle
Reconstruction of phylogenetic trees by maximum likelihood
Treeview
Java re-implementation of Michael Eisen's TreeView
Treeviewx
Displays and prints phylogenetic trees

Debian packages in contrib or non-free

Gmap
spliced and SNP-tolerant alignment for mRNA and short reads

Packaging has started and developers might try the packaging code in VCS

Forester
Graphical vizualiation tool Archaeopteryx
Patristic
Calculate patristic distances and comparing the components of genetic change

No known packages available but some record of interest (WNPP bug)

Phylowin
Graphical interface for molecular phylogenetic inference

No known packages available

Gbioseq
DNA sequence editor for Linux
Jstreeview
Editor for Phylogenetic Trees
Phpphylotree
draw phylogenetic trees
Treetime
Bayesian sampling of phylogenetic trees from molecular data

Cloud - Debian Med bioinformatics applications usable in cloud computing

This metapackage will install Debian packages related to molecular biology, structural biology and bioinformatics for use in life sciences, that do not depend on graphical toolkits and therefore can fit on system images for use in cloud computing clusters, where space can be limited.

Official Debian packages with high relevance

Abyss
de novo, parallel, sequence assembler for short reads
Acedb-other
retrieval of DNA or protein sequences
Aevol
digital genetics model to run Evolution Experiments in silico
Alien-hunter
Interpolated Variable Order Motifs to identify horizontally acquired DNA
Altree
program to perform phylogeny-based association and localization analysis
Amap-align
Protein multiple alignment by sequence annealing
Ampliconnoise
removal of noise from 454 sequenced PCR amplicons
Anfo
Short Read Aligner/Mapper from MPG
Aragorn
tRNA and tmRNA detection in nucleotide sequences
Arden
specificity control for read alignments using an artificial reference
Autodock
analysis of ligand binding to protein structure
Autodock-vina
docking of small molecules to proteins
Autogrid
pre-calculate binding of ligands to their receptor
Bamtools
toolkit for manipulating BAM (genome alignment) files
Bedtools
suite of utilities for comparing genomic features
Biomaj
biological data-bank updater
Bioperl
Perl tools for computational molecular biology
Bioperl-run
BioPerl wrappers: scripts
Biosquid
utilities for biological sequence analysis
Blast2
transitional dummy package to ncbi-blast+-legacy
Bowtie
Ultrafast memory-efficient short read aligner
Bowtie2
ultrafast memory-efficient short read aligner
Boxshade
Pretty-printing of multiple sequence alignments
Bwa
Burrows-Wheeler Aligner
Cain
simulations of chemical reactions
Cassiopee
index and search tool in genomic sequences
Cd-hit
suite of programs designed to quickly group sequences
Cdbfasta
Constant DataBase indexing and retrieval tools for multi-FASTA files
Circos
plotter for visualizing data
Clearcut
extremely efficient phylogenetic tree reconstruction
Clonalframe
inference of bacterial microevolution using multilocus sequence data
Clustalo
General purpose multiple sequence alignment program for proteins
Clustalw
global multiple nucleotide or peptide sequence alignment
Concavity
predictor of protein ligand binding sites from structure and conservation
Conservation-code
protein sequence conservation scoring tool
Datamash
statistics tool for command-line interface
Dialign
Segment-based multiple sequence alignment
Dialign-tx
Segment-based multiple sequence alignment
Discosnp
discovering Single Nucleotide Polymorphism from raw set(s) of reads
Disulfinder
cysteines disulfide bonding state and connectivity predictor
Dnaclust
tool for clustering millions of short DNA sequences
Dssp
protein secondary structure assignment based on 3D structure
Embassy-domainatrix
Extra EMBOSS commands to handle domain classification file
Embassy-domalign
Extra EMBOSS commands for protein domain alignment
Embassy-domsearch
Extra EMBOSS commands to search for protein domains
Emboss
European molecular biology open software suite
Exonerate
generic tool for pairwise sequence comparison
Fastdnaml
Tool for construction of phylogenetic trees of DNA sequences
Fastlink
faster version of pedigree programs of Linkage
Fastqc
quality control for high throughput sequence data
Fasttree
phylogenetic trees from alignments of nucleotide or protein sequences
Fastx-toolkit
FASTQ/A short nucleotide reads pre-processing tools
Filo
FILe and stream Operations
Fitgcp
fitting genome coverage distributions with mixture models
Flexbar
flexible barcode and adapter removal for sequencing platforms
Freecontact
fast protein contact predictor
Gasic
genome abundance similarity correction
Genometools
versatile genome analysis toolkit
Gff2aplot
pair-wise alignment-plots for genomic sequences in PostScript
Gff2ps
produces PostScript graphical output from GFF-files
Giira
RNA-Seq driven gene finding incorporating ambiguous reads
Glam2
gapped protein motifs from unaligned sequences
Grinder
Versatile omics shotgun and amplicon sequencing read simulator
Gromacs
Molecular dynamics simulator, with building and analysis tools
Hhsuite
sensitive protein sequence searching based on HMM-HMM alignment
Hmmer
profile hidden Markov models for protein sequence analysis
Idba
iterative De Bruijn Graph short read assemblers
Infernal
inference of RNA secondary structural alignments
Jellyfish
count k-mers in DNA sequences
Kalign
Global and progressive multiple sequence alignment
Kissplice
Detection of various kinds of polymorphisms in RNA-seq data
Last-align
genome-scale comparison of biological sequences
Loki
MCMC linkage analysis on general pedigrees
Macs
Model-based Analysis of ChIP-Seq on short reads sequencers
Mafft
Multiple alignment program for amino acid or nucleotide sequences
Mapsembler2
bioinformatics targeted assembly software
Maq
maps short fixed-length polymorphic DNA sequence reads to reference sequences
Melting
compute the melting temperature of nucleic acid duplex
Minia
short-read biological sequence assembler
Mipe
Tools to store PCR-derived data
Mira-assembler
Whole Genome Shotgun and EST Sequence Assembler
Mlv-smile
Find statistically significant patterns in sequences
Mothur
sequence analysis suite for research on microbiota
Mrbayes
Bayesian Inference of Phylogeny
Mummer
Efficient sequence alignment of full genomes
Muscle
Multiple alignment program of protein sequences
Mustang
multiple structural alignment of proteins
Ncbi-epcr
Tool to test a DNA sequence for the presence of sequence tagged sites
Ncbi-tools-bin
NCBI libraries for biology applications (text-based utilities)
Ncoils
coiled coil secondary structure prediction
Neobio
computes alignments of amino acid and nucleotide sequences
Paraclu
Parametric clustering of genomic and transcriptomic features
Parsinsert
Parsimonious Insertion of unclassified sequences into phylogenetic trees
Pdb2pqr
Preparation of protein structures for electrostatics calculations
Perm
efficient mapping of short reads with periodic spaced seeds
Phyml
Phylogenetic estimation using Maximum Likelihood
Phyutility
simple analyses or modifications on both phylogenetic trees and data matrices
Picard-tools
Command line tools to manipulate SAM and BAM files
Plink
whole-genome association analysis toolset
Poa
Partial Order Alignment for multiple sequence alignment
Prank
Probabilistic Alignment Kit for DNA, codon and amino-acid sequences
Prime-phylo
bayesian estimation of gene trees taking the species tree into account
Primer3
tool to design flanking oligo nucleotides for DNA amplification
Probabel
Toolset for Genome-Wide Association Analysis
Probcons
PROBabilistic CONSistency-based multiple sequence alignment
Proda
multiple alignment of protein sequences
Prodigal
Microbial (bacterial and archaeal) gene finding program
Pynast
alignment of short DNA sequences
Python-biopython
Python library for bioinformatics (implemented in Python 2)
Python-cogent
framework for genomic biology
Python3-biopython
Python library for bioinformatics (implemented in Python 3)
Qiime
Quantitative Insights Into Microbial Ecology
R-bioc-hilbertvis
GNU R package to visualise long vector data
R-cran-pvclust
Hierarchical Clustering with P-Values via Multiscale Bootstrap
R-cran-qtl
GNU R package for genetic marker linkage analysis
R-cran-vegan
Community Ecology Package for R
R-other-mott-happy.hbrem
GNU R package for fine-mapping complex diseases
Raster3d
tools for generating images of proteins or other molecules
Readseq
Conversion between sequence formats
Rnahybrid
Fast and effective prediction of microRNA/target duplexes
Rtax
Classification of sequence reads of 16S ribosomal RNA gene
Samtools
processing sequence alignments in SAM and BAM formats
Seqan-apps
C++ library for the analysis of biological sequences
Sibsim4
align expressed RNA sequences on a DNA template
Sigma-align
Simple greedy multiple alignment of non-coding DNA sequences
Sim4
tool for aligning cDNA and genomic DNA
Smalt
Sequence Mapping and Alignment Tool
Snap
location of genes from DNA sequence with hidden markov model
Soapdenovo
short-read assembly method to build de novo draft assembly
Soapdenovo2
short-read assembly method to build de novo draft assembly
Squizz
Converter for genetic sequences and alignments
Sra-toolkit
utilities for the NCBI Sequence Read Archive
Ssake
genomics application for assembling millions of very short DNA sequences
Staden-io-lib-utils
programs for maniuplating DNA sequencing files
T-coffee
Multiple Sequence Alignment
Tabix
generic indexer for TAB-delimited genome position files
Theseus
superimpose macromolecules using maximum likelihood
Tigr-glimmer
Gene detection in archea and bacteria
Tophat
fast splice junction mapper for RNA-Seq reads
Tree-ppuzzle
Parallelized reconstruction of phylogenetic trees by maximum likelihood
Tree-puzzle
Reconstruction of phylogenetic trees by maximum likelihood
Vcftools
Collection of tools to work with VCF files
Velvet
Nucleic acid sequence assembler for very short reads
Wise
comparison of biopolymers, like DNA and protein sequences
Zalign
parallel local alignment of biological sequences

Debian packages in contrib or non-free

Cufflinks
Transcript assembly, differential expression and regulation for RNA-Seq
Embassy-phylip
EMBOSS conversions of the programs in the phylip package
Gmap
spliced and SNP-tolerant alignment for mRNA and short reads

Packaging has started and developers might try the packaging code in VCS

Bagpipe
genomewide LD mapping
R-other-valdar-bagphenotype.library
GNU R extension of the functionality of happy

Content management - Debian Med content management systems

Here you can find software that is useful to build a content management system for medical care.

Packaging has started and developers might try the packaging code in VCS

Zope-zms
Content management for science, technology and medicine

No known packages available but some record of interest (WNPP bug)

Xnat
platform for data management and productivity tasks in neuroimaging

No known packages available

Hid
database management system for clinical imaging

Medical data - Debian Med drug databases

This metapackage will install free drug databases and related applications. The database can be accessed by any EMR using the application.

Official Debian packages with high relevance

Freediams
pharmaceutical drug prescription and interaction manager
Freemedforms-freedata
free extra-data for the FreeMedForms project
Python-hl7
Python library for parsing HL7 messages

Official Debian packages with lower relevance

Sleepyhead
Sleep tracking software with a focus on monitoring CPAP treatment

No known packages available

Drugref.org
pharmaceutical reference database

Dental - Debian Med packages related to dental practice

This metapackage contains dependencies for a collection of software which might be helpful for dentists to manage their practice.

Official Debian packages with high relevance

Entangle
Tethered Camera Control & Capture
Imagetooth
This library generates images of teeth for odontograms.
Openmolar
dental practice management software

Epidemiology - Debian Med epidemiology related packages

This metapackage will install tools that are useful in epidemiological research. Several packages making use of the GNU R data language for statistical investigation. It might be a good idea to read the paper "A short introduction to R for Epidemiology" at http://staff.pubhealth.ku.dk/%7Ebxc/Epi/R-intro.pdf

Official Debian packages with high relevance

Epigrass
scientific tool for simulations and scenario analysis in network epidemiology
Python-treetime
inference of time stamped phylogenies and ancestral reconstruction
R-cran-diagnosismed
medical diagnostic test accuracy analysis toolkit
R-cran-epi
GNU R epidemiological analysis
R-cran-epibasix
GNU R Elementary Epidemiological Functions
R-cran-epicalc
GNU R Epidemiological calculator
R-cran-epir
GNU R Functions for analysing epidemiological data
R-cran-epitools
GNU R Epidemiology Tools for Data and Graphics
R-cran-lexrankr
extractive summarization of text with the LexRank algorithm
R-cran-seroincidence
GNU R seroincidence calculator tool
R-cran-surveillance
GNU R package for the Modeling and Monitoring of Epidemic Phenomena

Official Debian packages with lower relevance

R-cran-cmprsk
GNU R subdistribution analysis of competing risks
R-cran-msm
GNU R Multi-state Markov and hidden Markov models in continuous time

Packaging has started and developers might try the packaging code in VCS

Netepi-analysis
network-enabled tools for epidemiology and public health practice
Netepi-collection
network-enabled tools for epidemiology and public health practice
Shiny-server
put Shiny web apps online
Ushahidi
web platform for information collection

No known packages available but some record of interest (WNPP bug)

Repast
framework for creating agent based simulations

Hospital information systems - Debian Med suggestions for Hospital Information Systems

This metapackage contains dependencies for software and that could be useful ro run a Hospital Information System. While there is continuous work going on to package a ready to install system currently only preconditions are finished but hopefully helpful in hospitals anyway.

Official Debian packages with high relevance

Fis-gtm
metapackage for the latest version of FIS-GT.M database
Orthanc-wsi
Whole-slide imaging support for Orthanc (digital pathology)

Packaging has started and developers might try the packaging code in VCS

Care2x
integrated hospital information system
Ewd-920
package for EWD Entrerprise Web Development platform.
Openmrs
enterprise electronic medical record system framework
Tryton-modules-health
Tryton Application Platform (Health Module)
Vista-foia
metapackage for the latest version of vista-foia.

Unofficial packages built by somebody else

Oscar-mcmaster
Oscar (Web) A medical web application for electronic medical records

No known packages available but some record of interest (WNPP bug)

World-vista
repackage and extended version of VistA produced by WorldVistA

No known packages available

Hkma-cms
clinic management system
Ipath
telemedicine platform
Openeyes
ophthalmology electronic patient record system
Openmaxims
patient administration system and electronic patient record
Patientos
Healthcare Information System (HIS) for small hospitals and clinics

Imaging - Debian Med image processing and visualization packages

This metapackage will install Debian packages which might be useful in medical image processing and visualization.

On one hand, it installs several packages supporting various image file formats and image management, like DICOM (Digital Imaging and Communications in Medicine) which is the de-facto standard for medical image management, and NIFTI. On the other hand, it provides a variety of software packages that can be used for visualization and for image processing - either from a graphical user interface, the command line, or implemented in workflows.

Official Debian packages with high relevance

Aeskulap
medical image viewer and DICOM network client
Amide
software for Medical Imaging
Ants
advanced normalization tools for brain and image analysis
Bart
tools for computational magnetic resonance imaging
Biosig-tools
format conversion tools for biomedical data formats
Camitk-imp
workbench application for the CamiTK library
Caret
Computerized Anatomical Reconstruction and Editing Toolkit
Conquest-common
ConQuest DICOM Server - common files
Ctn
Central Test Node, a DICOM implementation for medical imaging
Ctsim
Computed tomography simulator
Dcm2niix
next generation DICOM to NIfTI converter
Dcmtk
OFFIS DICOM toolkit command line utilities
Dicom3tools
DICOM medical image files manipulation and conversion tools
Dicomnifti
converts DICOM files into the NIfTI format
Dicomscope
OFFIS DICOM Viewer
Fslview
viewer for (f)MRI and DTI data
Fw4spl
FrameWork for Software Production Line
Gdf-tools
IO library for the GDF -- helper tools
Ginkgocadx
Medical Imaging Software and complete DICOM Viewer
Gofigure2
Tool for visualizing, processing and analysing of bioimages
Gwyddion
Scanning Probe Microscopy visualization and analysis tool
Imagej
Image processing program with a focus on microscopy images
Imagevis3d
desktop volume rendering application for large data
Invesalius
3D medical imaging reconstruction software
Ismrmrd-tools
command-line tools for ISMRMRD
Itksnap
semi-automatic segmentation of structures in 3D images
King
interactive system for three-dimensional vector graphics
Libgdcm-tools
Grassroots DICOM tools and utilities
Lipsia
analysis suite for MRI and fMRI data
Medcon
Medical Image (DICOM, ECAT, ...) conversion tool
Mia-tools
Command line tools for gray scale image processing
Mia-viewit
Viewer program for 3D data sets created by using MIA
Mialmpick
Tools for landmark picking in 3D volume data sets
Minc-tools
MNI medical image format tools
Mriconvert
medical image file conversion utility
Mricron
magnetic resonance image conversion, viewing and analysis
Mrtrix
diffusion-weighted MRI white matter tractography
Nifti-bin
tools shipped with the NIfTI library
Odin
develop, simulate and run magnetic resonance sequences
Openmeeg-tools
openmeeg library -- command line tools
Openslide-tools
Manipulation and conversion tools for OpenSlide
Orthanc
Lightweight, RESTful DICOM server for medical imaging
Orthanc-wsi
Whole-slide imaging support for Orthanc (digital pathology)
Pixelmed-apps
DICOM implementation containing Image Viewer and a ECG Viewer - jnlp
Plastimatch
medical image reconstruction and registration
Python-dicom
DICOM medical file reading and writing (Python 2)
Python-dipy
Python library for the analysis of diffusion MRI datasets
Python-mvpa2
multivariate pattern analysis with Python v. 2
Python-nibabel
Python bindings to various neuroimaging data formats
Python-nipy
Analysis of structural and functional neuroimaging data
Python-nipype
Neuroimaging data analysis pipelines in Python
Python-nitime
timeseries analysis for neuroscience data (nitime)
Python-surfer
visualize Freesurfer's data in Python
Python-tifffile
Read and write image data from and to TIFF files
Sigviewer
GUI viewer for biosignals such as EEG, EMG, and ECG
Slicer
software package for visualization and image analysis - main application
Sofa-apps
GUI for the Simulation Open Framework Architecture (SOFA)
Teem-apps
Tools to process and visualize scientific data and images - command line tools
Via-bin
tools for volumetric image analysis
Volview
Advanced volume visualization tool
Voxbo
processing, statistical analysis, and display of brain imaging data
Vtk-dicom-tools
DICOM for VTK - tools
Xmedcon
Medical Image (DICOM, ECAT, ...) conversion tool (GUI)

Official Debian packages with lower relevance

Cmtk
Computational Morphometry Toolkit
Connectomeviewer
Interactive Analysis and Visualization for MR Connectomics
Conquest-dbase
ConQuest DICOM Server - DBaseIII backend
Conquest-mysql
ConQuest DICOM Server - MySQL backend
Conquest-postgres
ConQuest DICOM Server - PostgreSQL backend
Conquest-sqlite
ConQuest DICOM Server - SQLite backend
Elastix
toolbox for rigid and nonrigid registration of images
Imagemagick
image manipulation programs -- binaries
Imview
Image viewing and analysis application
Openwalnut-qt4
Multi-modal medical and brain data visualization tool.
Orthanc-dicomweb
Plugin to extend Orthanc with support of WADO and DICOMweb
Orthanc-imagej
ImageJ plugin to import images from Orthanc
Orthanc-postgresql
Plugins to use PostgreSQL as a database back-end to Orthanc
Orthanc-webviewer
Web viewer of medical images for Orthanc
Paraview
Parallel Visualization Application
Pngquant
PNG (Portable Network Graphics) image optimising utility
Python-pyxid
interface for Cedrus XID and StimTracker devices
Science-workflow
workflow management systems useful for scientific research
Trimage
GUI and command-line interface to optimize image files

Debian packages in contrib or non-free

Fsl
transitional dummy package
Vmtk
the Vascular Modeling Toolkit

Packaging has started and developers might try the packaging code in VCS

Afni
toolkit for analyzing and visualizing functional MRI data
Bart-view
viewer for multi-dimensional complex-valued data
Bioimagesuite
integrated image analysis software suite
Bioimagexd
Analyzing, processing and visualizing of multi dimensional microscopy images
Cellprofiler
quantitatively measure phenotypes from images automatically
Crea
base library of the creaTools medical image processing suite
Dicoogle
Java Advanced Imaging API reference implementation
Freesurfer
analysis and visualization of functional brain imaging data
Incf-nidash-oneclick-clients
utility for pushing DICOM data to the INCF datasharing server
Insightapplications
InsightToolKit (ITK) based medical imaging applications
Jist
Java Image Science Toolkit
Kradview
medical image viewer for DICOM images
Libdcm4che-java
Clinical Image and Object Management
Mayam
Cross-platform DICOM Viewer
Micromanager
Microscopy Software
Mipav
quantitative analysis and visualization of medical images
Mni-colin27-nifti
Talairach stereotaxic space template
Openelectrophy
data analysis GUI for intra- and extra-cellular recordings
Stabilitycalc
evaluate fMRI scanner stability
Visit
interactive parallel visualization and graphical analysis tool

Unofficial packages built by somebody else

Cdmedicpacs
web interface to PACS to access DICOM study images
Fiji
The Fiji image processing suite (based on ImageJ)
Mni-autoreg
MNI average brain (305 MRI) stereotaxic registration model
Mni-n3
MNI Non-parametric Non-uniformity Normalization
Opendicom.net
API to DICOM in C# for Mono

No known packages available but some record of interest (WNPP bug)

Devide
Delft Visualization and Image processing Development Environment
Dtitk
DTI spatial normalization and atlas construction toolkit
Eeglab
toolbox for processing and visualization of electrophysiological data
Isis
I/O framework for neuroimaging data
Jemris
high performance computing MRI simulator
Opensourcepacs
medical image referral, archiving, routing and viewing system
Xnat
platform for data management and productivity tasks in neuroimaging

No known packages available

Blox
medical imaging and visualization program
Brainvisa
image processing factory for MR images
Dcm4chee
Clinical Image and Object Management (enterprise)
Dicom4j
Java framework for Dicom
Drjekyll
interactive voxel editor for viewing and editing three-dimensional images
Dti-query
dynamic queries of the white matter brain pathways
Ecg2png
convert scanned electrocardiograms into PNG format
Gimias
Graphical Interface for Medical Image Analysis and Simulation
Hid
database management system for clinical imaging
Maris
package suite for Radiological Workflow
Medisnap
photograph, manage, view, compare, document and archive medical photos
Mesa-test-tools
IHE Test Software for Radiology
Miview
Medical Images viewer and converter
Mni-icbm152-nlin-2009
MNI stereotaxic space human brain template
Mrisim
simulator for magnetic resonance imaging data
Omero
coming standard LIMS for microscopy images
Piano
medical image processing library for surgical planning
Pymeg
suite for analysis of magnetoencephalography (MEG) data
Stir
Software for Tomographic Image Reconstruction
Tempo
3D visualization of brain electrical activity

Imaging development - Debian Med image processing and visualization packages development

This metapackage will install Debian packages which might be useful for developing applications for medical image processing and visualization.

Official Debian packages with high relevance

Cimg-dev
powerful image processing library
Ctn-dev
Development files for Central Test Node, a DICOM implementation
Gmic
GREYC's Magic for Image Computing
Libbart-dev
Development files for BART
Libbiosig-dev
I/O library for biomedical data - development files
Libcamitk-dev
Computer Assisted Medical Intervention Tool Kit - development
Libcifti-dev
development files for CiftiLib
Libcv-dev
Translation package for libcv-dev
Libedf-dev
European Data Format library - devel
Libgdf-dev
IO library for the GDF -- development library
Libgiftiio-dev
IO library for the GIFTI cortical surface data format
Libigstk4-dev
Toolkit for image-guided surgery applications - development
Libinsighttoolkit4-dev
Image processing toolkit for registration and segmentation - development
Libismrmrd-dev
development files for ISMRMRD
Libmaxflow-dev
Development files for the maxflow-mincut algorithm
Libmdc2-dev
Medical Image (DICOM, ECAT, ...) conversion tool (development)
Libmia-2.4-dev
library for 2D and 3D gray scale image processing, development files
Libmialm-dev
Development files for the MIA landmark library
Libmiaviewit-dev
development files for the 3D visualization library
Libminc-dev
MNI medical image format development environment
Libnifti-dev
IO libraries for the NIfTI-1 data format
Libodil0-dev
C++11 library for the DICOM standard (development files)
Libopenigtlink-dev
Open IGT Link is a simple network protocol - development
Libopenmeeg-dev
openmeeg library -- development files
Libopenslide-dev
Development files for the OpenSlide library
Libopensurgsim-dev
Free platform for surgical simulation - development
Libpapyrus3-dev
DICOM compatible file format library
Libteem-dev
Tools to process and visualize scientific data and images - development
Libvia-dev
library for volumetric image analysis
Libvigraimpex-dev
development files for the C++ computer vision library
Libvistaio-dev
Development files for the libvistaio library
Libvolpack1-dev
fast volume rendering library (development package)
Libvtk-dicom-dev
DICOM for VTK - dev
Libvtk-dicom-java
DICOM for VTK - java
Libvtk6-dev
VTK header files
Libvxl1-dev
C++ Libraries for Computer Vision Research (development files)
Octave-bart
Octave bindings for BART
Octave-gdf
IO library for the GDF -- Octave interface
Odin
develop, simulate and run magnetic resonance sequences
Python-casmoothing
Context-aware mesh smoothing for biomedical applications
Python-cfflib
Multi-modal connectome and metadata management and integration
Python-dicom
DICOM medical file reading and writing (Python 2)
Python-dipy
Python library for the analysis of diffusion MRI datasets
Python-gdcm
Grassroots DICOM Python bindings
Python-imageio
library for reading and writing image data (Python 2)
Python-mia
Python-2 bindings for the MIA image processing library
Python-mne
Python modules for MEG and EEG data analysis
Python-mvpa2
multivariate pattern analysis with Python v. 2
Python-nibabel
Python bindings to various neuroimaging data formats
Python-nipy
Analysis of structural and functional neuroimaging data
Python-nipype
Neuroimaging data analysis pipelines in Python
Python-nitime
timeseries analysis for neuroscience data (nitime)
Python-openslide
Python 2 wrapper for reading whole slide image files
Python-pyxnat
Interface to access neuroimaging data on XNAT servers
Python-vigra
Python bindings for the C++ computer vision library
Python3-mia
Python-3 bindings for the MIA image processing library
R-cran-rniftilib
GNU/R interface to NIFTICLIB

Official Debian packages with lower relevance

Igstk-examples
Toolkit for image-guided surgery applications - examples
Libcamp-dev
C++ multi-purpose reflection library (development files)
Libeegdev-dev
Biosignal acquisition device library (Developement files)
Libfreeimage-dev
Support library for graphics image formats (development files)
Libics-dev
Image Cytometry Standard file reading and writing
Liblimereg-dev
Library for lightweight image registration [development files]
Libnifti-doc
NIfTI library API documentation
Libvtkedge-dev
Library of advanced visualization and data processing techniques - development
Libxdffileio-dev
Library to read/write EEG data file formats (development files)
Python-libavg
High-level development platform for media-centric applications
Python-tifffile
Read and write image data from and to TIFF files

Debian packages in contrib or non-free

Libvmtk-dev
shared links and header files for vmtk
Python-vmtk
Python interface for vmtk

Packaging has started and developers might try the packaging code in VCS

Emokit
Emotiv EPOC headset Python interface
Libbio-formats-java
reading and writing proprietary microscopy image data and metadata
Libctk-dev
toolkit for medical imaging application development - devel
Libopenslide-java
java wrapper for reading whole slide image files

Unofficial packages built by somebody else

Libmni-perllib-perl
The MNI Perl Library

No known packages available

Octave-dicom
Dicom support in Octave

Laboratory - Debian Med suggestions for medical laboratories

This metapackage contains dependencies for software and that could be useful ro run a medical laboratory.

Official Debian packages with high relevance

Opencfu
count cell colonies (CFUs) on agar plates by processing digital pictures
Orthanc-wsi
Whole-slide imaging support for Orthanc (digital pathology)

Packaging has started and developers might try the packaging code in VCS

Openfreezer
Laboratory analysis, research and investigation software application

No known packages available

Catissuesuite
tool for biospecimen inventory management
Openelis
Enterprise Laboratory Information System

Oncology - Debian Med packages for oncology

This metapackage will install tools that are useful for radiation oncology.

Official Debian packages with high relevance

Dicompyler
radiation therapy research platform
Orthanc-wsi
Whole-slide imaging support for Orthanc (digital pathology)

Packaging has started and developers might try the packaging code in VCS

Uw-prism
software tools for radiation therapy planning

No known packages available

Planunc
tools for radiotherapy treatment planning

Pharmacology - Debian Med packages for pharmaceutical research

This metapackage contains dependencies for a collection of software and documentation which is useful for pharmaceutical research.

Official Debian packages with high relevance

Chemtool
chemical structures drawing program
R-cran-dosefinding
Planning and Analyzing Dose Finding experiments

Debian packages in contrib or non-free

Raccoon
preparation of in silico drug screening projects

Physics - Debian Med packages for medical physicists

This metapackage contains dependencies for a collection of software and documentation which is useful for medical physicists in radiation oncology, diagnostics imaging and related fields.

Official Debian packages with high relevance

Biosig-tools
format conversion tools for biomedical data formats
Gdf-tools
IO library for the GDF -- helper tools
Octave
GNU Octave language for numerical computations
Paw
Physics Analysis Workstation - a graphical analysis program
Paw++
Physics Analysis Workstation (Lesstif-enhanced version)
R-base
GNU R statistical computation and graphics system

Official Debian packages with lower relevance

Libbiosig-dev
I/O library for biomedical data - development files
Octave-biosig
Octave bindings for BioSig library
Paw-demos
Physics Analysis Workstation examples and tests
Python-biosig
Python bindings for BioSig library
Python-multipletau
multiple-tau algorithm for Python/NumPy

No known packages available but some record of interest (WNPP bug)

Gate
Geant4 Application for Emission Tomography
Openvibe
platform for the design, test and use of BCI

Practice - Debian Med packages for practice management

This metapackage contains dependencies for a collection of software which might be helpful for practitioners to manage their practice.

Official Debian packages with high relevance

Entangle
Tethered Camera Control & Capture
Freediams
pharmaceutical drug prescription and interaction manager
Freemedforms-emr
electronic medical record manager
Ginkgocadx
Medical Imaging Software and complete DICOM Viewer
Gnumed-client
medical practice management - Client
Gnumed-server
medical practice management - server
Libchipcard-tools
tools for accessing chipcards
Orthanc
Lightweight, RESTful DICOM server for medical imaging
Orthanc-wsi
Whole-slide imaging support for Orthanc (digital pathology)
Qrisk2
cardiovascular disease risk calculator
R-cran-medadherence
GNU R Medication Adherence: Commonly Used Definitions
Sleepyhead
Sleep tracking software with a focus on monitoring CPAP treatment

Official Debian packages with lower relevance

Libctapimkt1
Read German Krankenversichertenkarte and eGK

Packaging has started and developers might try the packaging code in VCS

Openemr
Comprehensive medical practice management
Thera-pi
organization and management of outpatient clinics and rehabilitation-medicine companies

Unofficial packages built by somebody else

Elementalclinic
Electronical Medical Health record system for mental health
Freemed
Electronic Medical Record and Practice Management system
Freeshim
opensource electronic medical device interface
Tinyheb
billing system for midwives

No known packages available but some record of interest (WNPP bug)

Elexis
medical practice managemant system for use in Switzerland
Openrep
software for homeopathic repertorization and viewing materia medicae

No known packages available

Clearhealth
Medical practice management system
Freeb
Medical Bill formating module
Medintux
Medical practice management system
Mirrormed
EHR and practice management system
Mirth
HL7 integration engine
Openpms
medical billing, scheduling, and account management system
Proteus
clinical decision support guidelines model
Remitt
preparing and submitting medical billing data
Resmedicinae
comprising software solution for use in medicine
Sqlclinic
intranet solution for Saint Vincents Catholic Medical Centers of New York

Psychology - Debian Med packages for psychology

This metapackage contains dependencies for a collection of software which might be helpful for psychological research.

Official Debian packages with high relevance

Praat
program for speech analysis and synthesis
Psignifit
Fitting and testing hypotheses about psychometric functions
Psychopy
environment for creating psychology stimuli in Python
Python-pyepl
module for coding psychology experiments in Python
Python-pypsignifit
psychometric analysis of psychophysics data in Python
R-cran-foreign
GNU R package to read/write data from other stat. systems
R-cran-psy
GNU R procedures for psychometrics

Official Debian packages with lower relevance

Python-visionegg
Python library for 2D/3D visual stimulus generation
Science-psychophysics
Debian Science packages for Psychophysics

Unofficial packages built by somebody else

Miscpsycho
Miscellaneous Psychometric Analyses
Psych
Procedures for Psychological, Psychometric, and Personality Research
Psychometric
Applied Psychometric Theory
Psychotree
Recursive Partitioning Based on Psychometric Models
Psyphy
Functions for analyzing psychophysical data in R

Rehabilitation - Debian Med packages for rehabilitation technologies

This metapackage will install tools that are useful for rehabilitation and therapy.

Official Debian packages with high relevance

Sitplus
Free software framework for ludic-therapeutic activities

Official Debian packages with lower relevance

Aghermann
Sleep-research experiment manager

Research - Debian Med packages for medical research

This metapackage will install tools that are useful for medical research.

No known packages available but some record of interest (WNPP bug)

Openclinica
electronic data capture and clinical data management

Statistics - Debian Med statistics

This metapackage will install packages which are helpful to do statistics with a special focus on tasks in medical care.

Official Debian packages with high relevance

R-bioc-limma
linear models for microarray data
R-bioc-multtest
Bioconductor resampling-based multiple hypothesis testing
R-bioc-qvalue
GNU R package for Q-value estimation for FDR control
R-cran-ade4
GNU R analysis of ecological data
R-cran-beeswarm
bee swarm plot, an alternative to stripchart
R-cran-pvclust
Hierarchical Clustering with P-Values via Multiscale Bootstrap
R-cran-randomforest
GNU R package implementing the random forest classificator

Official Debian packages with lower relevance

Science-statistics
Debian Science Statistics packages

Packaging has started and developers might try the packaging code in VCS

Rstudio
GNU R IDE

Tools - Debian Med several tools

This metapackage will install tools for several purposes in health care. Currently it contains some simple programs for Personal Health.

Official Debian packages with high relevance

Cronometer
CRON-o-Meter - Exercise and nutrient intake tracker
Edfbrowser
viewer for biosignal storage files such as bdf and edf
Galileo
Utility to securely synchronize a Fitbit device with the Fitbit web service
Hunspell-de-med
German medical dictionary for hunspell
Hunspell-en-med
English medical dictionary for hunspell
Nut-nutrition
dietary nutrition analysis software
Nutsqlite
Dietary nutrition analysis software
Pcalendar
track menstrual cycles and predict fertility periods
Pondus
personal weight manager for GTK+2
Python-clips
Python module to interface the CLIPS expert system shell library
Python-fitbit
FitBit REST API Client Implementation
Quitcount
Small tool which may help yourself quit smoking
R-cran-fitbitscraper
Import your Fitbit data from the Fitbit's website into R
R-cran-fitcoach
R package for analysis and retrieve data of Fitbit
Wgerman-medical
German medical dictionary words for /usr/share/dict
Workrave
Repetitive Strain Injury prevention tool

Official Debian packages with lower relevance

Cycle
calendar program for women
Entangle
Tethered Camera Control & Capture
Goldencheetah
set of analysis tools for cycling performance
Mencal
menstruation calendar
Sleepyhead
Sleep tracking software with a focus on monitoring CPAP treatment

Debian packages in contrib or non-free

Mssstest
Normalisation of disease scores for patients with Multiple Sclerosis

Packaging has started and developers might try the packaging code in VCS

Pesco
Cognitive stimulation tool for elderly or cognitively impaired

Typesetting - Debian Med support for typesetting and publishing

This metapackage will install Debian packages that might be helpful for typesetting and publishing in medical care and structural biology.

Official Debian packages with high relevance

King
interactive system for three-dimensional vector graphics
Texlive-latex-extra
TeX Live: LaTeX additional packages
Texlive-science
TeX Live: Mathematics, natural sciences, computer science packages

Official Debian packages with lower relevance

Biber
Much-augmented BibTeX replacement for BibLaTeX users
Bibus
bibliographic database
Jabref-plugin-oo
LibreOffice plugin for JabRef (transitional dummy package)
Kbibtex
BibTeX editor for KDE
R-cran-qqman
R package for visualizing GWAS results using Q-Q and manhattan plots
Referencer
GNOME Document Organiser