Package: med-cloud (3.8.1)

[ Source: debian-med  ]

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.

Tags: Field: Molecular Biology, Role: Metapackage

Other Packages Related to med-cloud

• dep: med-config (= 3.8.1)

  Debian Med general config package

• dep: med-tasks (= 3.8.1)

  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: 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: muscle3

  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: python3-cogent3

  framework for genomic biology

• 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

• sug: anfo

  Short Read Aligner/Mapper from MPG

• 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

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