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[ Source: debian-med  ]

Links for med-cloud

Ubuntu Resources:

• Bug Reports
• Ubuntu Changelog
• Copyright File

Download Source Package debian-med:

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

Maintainer:

• Ubuntu MOTU Developers (Mail Archive)

Please consider filing a bug or asking a question via Launchpad before contacting the maintainer directly.

Original Maintainers (usually from Debian):

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

It should generally not be necessary for users to contact the original maintainer.

Similar packages:

• med-bio
• med-statistics
• med-data
• med-tools
• med-config
• med-epi
• med-oncology
• med-psychology
• med-tasks
• med-laboratory
• med-pharmacy

Other Packages Related to med-cloud

depends

recommends

suggests

enhances

• dep: med-config (= 3.7.1)

  Debian Med general config package

• dep: med-tasks (= 3.7.1)

  Debian Med tasks for tasksel

• rec: abyss

  de novo, parallel, sequence assembler for short reads

• rec: acedb-other

  retrieval of DNA or protein sequences

• rec: aevol

  digital genetics model to run Evolution Experiments in silico

• rec: alien-hunter

  Interpolated Variable Order Motifs to identify horizontally acquired DNA

• rec: altree

  program to perform phylogeny-based association and localization analysis

• rec: amap-align

  Protein multiple alignment by sequence annealing

• rec: ampliconnoise

  removal of noise from 454 sequenced PCR amplicons

• rec: anfo

  Short Read Aligner/Mapper from MPG

• rec: aragorn

  tRNA and tmRNA detection in nucleotide sequences

• rec: arden

  specificity control for read alignments using an artificial reference

• rec: autodock

  analysis of ligand binding to protein structure

• rec: autodock-vina

  docking of small molecules to proteins

• rec: autogrid

  pre-calculate binding of ligands to their receptor

• rec: bamtools

  toolkit for manipulating BAM (genome alignment) files

• rec: bedtools

  suite of utilities for comparing genomic features

• rec: bioperl

  Perl tools for computational molecular biology

• rec: bioperl-run

  BioPerl wrappers: scripts

• rec: biosquid

  utilities for biological sequence analysis

• rec: bowtie

  Ultrafast memory-efficient short read aligner

• rec: bowtie2

  ultrafast memory-efficient short read aligner

• rec: boxshade

  Pretty-printing of multiple sequence alignments

• rec: bwa

  Burrows-Wheeler Aligner

• rec: cassiopee

  index and search tool in genomic sequences

• rec: cd-hit

  suite of programs designed to quickly group sequences

• rec: cdbfasta

  Constant DataBase indexing and retrieval tools for multi-FASTA files

• rec: circos

  plotter for visualizing data

• rec: clearcut

  extremely efficient phylogenetic tree reconstruction

• rec: clonalframe

  inference of bacterial microevolution using multilocus sequence data

• rec: clustalo

  General-purpose multiple sequence alignment program for proteins

• rec: clustalw

  global multiple nucleotide or peptide sequence alignment

• rec: concavity

  predictor of protein ligand binding sites from structure and conservation

• rec: conservation-code

  protein sequence conservation scoring tool

• rec: datamash

  statistics tool for command-line interface

• rec: dialign

  Segment-based multiple sequence alignment

• rec: dialign-tx

  Segment-based multiple sequence alignment

• rec: discosnp

  discovering Single Nucleotide Polymorphism from raw set(s) of reads

• rec: disulfinder

  cysteines disulfide bonding state and connectivity predictor

• rec: dnaclust

  tool for clustering millions of short DNA sequences

• rec: dssp

  protein secondary structure assignment based on 3D structure

• rec: embassy-domainatrix

  Extra EMBOSS commands to handle domain classification file

• rec: embassy-domalign

  Extra EMBOSS commands for protein domain alignment

• rec: embassy-domsearch

  Extra EMBOSS commands to search for protein domains

• rec: emboss

  European molecular biology open software suite

• rec: exonerate

  generic tool for pairwise sequence comparison

• rec: fastdnaml

  Tool for construction of phylogenetic trees of DNA sequences

• rec: fastlink

  faster version of pedigree programs of Linkage

• rec: fastqc

  quality control for high throughput sequence data

• rec: fasttree

  phylogenetic trees from alignments of nucleotide or protein sequences

• rec: fitgcp

  fitting genome coverage distributions with mixture models

• rec: flexbar

  flexible barcode and adapter removal for sequencing platforms

• rec: freecontact

  fast protein contact predictor

• rec: gasic

  genome abundance similarity correction

• rec: genometools

  versatile genome analysis toolkit

• rec: gff2aplot

  pair-wise alignment-plots for genomic sequences in PostScript

• rec: gff2ps

  produces PostScript graphical output from GFF-files

• rec: glam2

  gapped protein motifs from unaligned sequences

• rec: gmap

  spliced and SNP-tolerant alignment for mRNA and short reads

• rec: grinder

  Versatile omics shotgun and amplicon sequencing read simulator

• rec: gromacs

  Molecular dynamics simulator, with building and analysis tools

• rec: hhsuite

  sensitive protein sequence searching based on HMM-HMM alignment

• rec: hisat2

  graph-based alignment of short nucleotide reads to many genomes

• rec: hmmer

  profile hidden Markov models for protein sequence analysis

• rec: idba

  iterative De Bruijn Graph short read assemblers

• rec: infernal

  inference of RNA secondary structural alignments

• rec: jellyfish

  count k-mers in DNA sequences

• rec: kalign

  Global and progressive multiple sequence alignment

• rec: kissplice

  Detection of various kinds of polymorphisms in RNA-seq data

• rec: last-align

  genome-scale comparison of biological sequences

• rec: loki

  MCMC linkage analysis on general pedigrees

• rec: macs

  Model-based Analysis of ChIP-Seq on short reads sequencers

• rec: mafft

  Multiple alignment program for amino acid or nucleotide sequences

• rec: mapsembler2

  bioinformatics targeted assembly software

• rec: maq

  maps short fixed-length polymorphic DNA sequence reads to reference sequences

• rec: melting

  compute the melting temperature of nucleic acid duplex

• rec: minia

  short-read biological sequence assembler

• rec: mipe

  Tools to store PCR-derived data

• rec: mira-assembler

  Whole Genome Shotgun and EST Sequence Assembler

• rec: mlv-smile

  Find statistically significant patterns in sequences

• rec: mothur

  sequence analysis suite for research on microbiota

• rec: mrbayes

  Bayesian Inference of Phylogeny

• rec: mummer

  Efficient sequence alignment of full genomes

• rec: muscle

  Multiple alignment program of protein sequences

• rec: mustang

  multiple structural alignment of proteins

• rec: ncbi-epcr

  Tool to test a DNA sequence for the presence of sequence tagged sites

• rec: ncbi-tools-bin

  NCBI libraries for biology applications (text-based utilities)

• rec: ncoils

  coiled coil secondary structure prediction

• rec: neobio

  computes alignments of amino acid and nucleotide sequences

• rec: paraclu

  Parametric clustering of genomic and transcriptomic features

• rec: parsinsert

  Parsimonious Insertion of unclassified sequences into phylogenetic trees

• rec: pdb2pqr

  Preparation of protein structures for electrostatics calculations

• rec: perm

  efficient mapping of short reads with periodic spaced seeds

• rec: phyml

  Phylogenetic estimation using Maximum Likelihood

• rec: phyutility

  simple analyses or modifications on both phylogenetic trees and data matrices

• rec: picard-tools

  Command line tools to manipulate SAM and BAM files

• rec: plink

  whole-genome association analysis toolset

• rec: plink1.9

  whole-genome association analysis toolset

• rec: plink2

  whole-genome association analysis toolset

• rec: poa

  Partial Order Alignment for multiple sequence alignment

• rec: prank

  Probabilistic Alignment Kit for DNA, codon and amino-acid sequences

• rec: prime-phylo

  bayesian estimation of gene trees taking the species tree into account

• rec: primer3

  tool to design flanking oligo nucleotides for DNA amplification

• rec: probabel

  Toolset for Genome-Wide Association Analysis

• rec: probcons

  PROBabilistic CONSistency-based multiple sequence alignment

• rec: proda

  multiple alignment of protein sequences

• rec: prodigal

  Microbial (bacterial and archaeal) gene finding program

• rec: python3-biomaj3-cli

  BioMAJ client

• rec: python3-biopython

  Python3 library for bioinformatics

• rec: qiime

  Quantitative Insights Into Microbial Ecology

• rec: r-bioc-edger

  Empirical analysis of digital gene expression data in R

• rec: r-bioc-hilbertvis

  GNU R package to visualise long vector data

• rec: r-cran-pvclust

  Hierarchical Clustering with P-Values via Multiscale Bootstrap

• rec: r-cran-qtl

  GNU R package for genetic marker linkage analysis

• rec: r-cran-vegan

  Community Ecology Package for R

• rec: r-other-mott-happy.hbrem

  GNU R package for fine-mapping complex diseases

• rec: raster3d

  tools for generating images of proteins or other molecules

• rec: readseq

  Conversion between sequence formats

• rec: rnahybrid

  Fast and effective prediction of microRNA/target duplexes

• rec: rtax

  Classification of sequence reads of 16S ribosomal RNA gene

• rec: samtools

  processing sequence alignments in SAM, BAM and CRAM formats

• rec: seqan-apps

  C++ library for the analysis of biological sequences

• rec: sibsim4

  align expressed RNA sequences on a DNA template

• rec: sigma-align

  Simple greedy multiple alignment of non-coding DNA sequences

• rec: sim4

  tool for aligning cDNA and genomic DNA

• rec: smalt

  Sequence Mapping and Alignment Tool

• rec: snap

  location of genes from DNA sequence with hidden markov model

• rec: soapdenovo

  short-read assembly method to build de novo draft assembly

• rec: soapdenovo2

  short-read assembly method to build de novo draft assembly

• rec: squizz

  Converter for genetic sequences and alignments

• rec: sra-toolkit

  utilities for the NCBI Sequence Read Archive

• rec: ssake

  genomics application for assembling millions of very short DNA sequences

• rec: staden-io-lib-utils

  programs for manipulating DNA sequencing files

• rec: t-coffee

  Multiple Sequence Alignment

• rec: tabix

  generic indexer for TAB-delimited genome position files

• rec: theseus

  superimpose macromolecules using maximum likelihood

• rec: tigr-glimmer

  Gene detection in archea and bacteria

• rec: tree-puzzle

  Reconstruction of phylogenetic trees by maximum likelihood

  or tree-ppuzzle

  Parallelized reconstruction of phylogenetic trees by maximum likelihood

• rec: vcftools

  Collection of tools to work with VCF files

• rec: velvet

  Nucleic acid sequence assembler for very short reads

• rec: wise

  comparison of biopolymers, like DNA and protein sequences

• rec: zalign

  parallel local alignment of biological sequences

• sug: bagpipe

  Package not available

• sug: blast2

  Package not available

• sug: cufflinks

  Transcript assembly, differential expression and regulation for RNA-Seq

• sug: embassy-phylip

  Package not available

• sug: giira

  Package not available

• sug: python3-cogent3

  framework for genomic biology

Download med-cloud

Download for all available architectures

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