Package: med-cloud (2.0)

[ 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 (= 2.0)

  Debian Med general config package

• dep: med-tasks (= 2.0)

  Debian Med tasks for tasksel

• 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: biomaj

  biological data-bank updater

• rec: bioperl

  Perl tools for computational molecular biology

• rec: bioperl-run

  BioPerl wrappers: scripts

• rec: biosquid

  utilities for biological sequence analysis

• rec: blast2

  Basic Local Alignment Search Tool

• 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: cain

  simulations of chemical reactions

• 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: concavity

  predictor of protein ligand binding sites from structure and conservation

• rec: datamash

  statistics tool for command-line interface

• 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: 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: fastx-toolkit

  FASTQ/A short nucleotide reads pre-processing tools

• rec: filo

  FILe and stream Operations

• 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: giira

  RNA-Seq driven gene finding incorporating ambiguous reads

• rec: grinder

  Versatile omics shotgun and amplicon sequencing read simulator

• rec: idba

  iterative De Bruijn Graph De Novo short read assembler for transcriptome

• rec: infernal

  inference of RNA secondary structural alignments

• 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: 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: mothur

  sequence analysis suite for research on microbiota

• 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: parsinsert

  Parsimonious Insertion of unclassified sequences into phylogenetic trees

• 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: primer3

  Tool to design flanking oligo nucleotides for DNA amplification

• rec: python-cogent

  framework for genomic biology

• 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 and BAM formats

• rec: smalt

  Sequence Mapping and Alignment Tool

• rec: ssake

  genomics application for assembling millions of very short DNA sequences

• rec: tophat

  fast splice junction mapper for RNA-Seq reads

• rec: velvet

  Nucleic acid sequence assembler for very short reads

• sug: abyss

  de novo, parallel, sequence assembler for short reads

• sug: bagpipe

  Package not available

• sug: cufflinks

  Transcript assembly, differential expression and regulation for RNA-Seq

Download med-cloud

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Architecture	Package Size	Installed Size	Files
all	12.3 kB	62.0 kB	[list of files]