软件版本描述

abyss1.9.0de novo, parallel, sequence assembler for short reads

ampliconnoise1.29Programs for the removal of noise from 454 sequenced PCR amplicons

arb5.5No description

archaeopteryx0.972.beta9MA phylogenetic tree viewer and editor

artemis16.0.0Free genome viewer and annotation tool

assembly-conversion-tools0.01Conversion tools for handling 454 assemblies.

axiome1.7biolinux1QIIME and mothur automation toolkit

axiome-dev1.7biolinux1QIIME automation toolkit — Plugin Development

backups0.3Bio-Linux 5/6/7 backup utilities.

bamtools2.4.0+dfsgtoolkit for manipulating BAM (genome alignment) files

beam20.1+20101008SNP-SNP interaction association mapping based on SNP-block models

bedtools2.17.0suite of utilities for comparing genomic features

berkeley-express1.5.1Streaming quantification for high-throughput sequencing

big-blast1.0.3The big-blast script for annotation of long sequences

biocode2.3.3Biocode plugin for Geneious workbench

bioperl1.6.923Perl tools for computational molecular biology

bioperl-run1.6.9BioPerl wrappers: scripts

biosquid1.9g+cvs20050121utilities for biological sequence analysis

bitseq0.7.0Bayesian Inference of Transcripts from Sequencing Data

blast21:2.2.26.20120620Basic Local Alignment Search Tool

bldp-files1.1Documentation for bioinformatics software on Bio-Linux.

blimps-utils3.9blocks database improved searcher

blixem3.1.1Interactive browser for viewing pairwise Blast results.

bowtie1.1.1Ultrafast memory-efficient short read aligner

bowtie22.2.6ultrafast memory-efficient short read aligner

bowtie2-debug2.2.6ultrafast memory-efficient short read aligner

bwa0.7.12Burrows-Wheeler Aligner

cap320080520A base calling system

catchall3.0.1Analyze data about microbial species abundance

cd-hit2009-1020a suite of programs designed to quickly group sequences

cdbfasta20100722Constant DataBase indexing and retrieval tools for multi-FASTA files

chimeraslayer20101212+dfsgdetects likely chimeras in PCR amplified DNA

clcsequenceviewer6.4CLC Free Sequence Viewer

clearcut1.0.9Relaxed Neighbor Joining

clustalw2.1+lgplNo description

clustalx2.1+lgplNo description

cortex-con0.05efficient and low-memory software for consensus genome assembly

cruft-killer0.3Remove cruft from Bio-Linux desktop

cufflinks2.2.1Transcript assembly, differential expression and regulation for RNA-Seq

cytoscape1:3.2.1Platform for visualizing complex-networks and integrating these with attribute data

dendroscope1.4.0Interactive viewer for large phylogenetic trees.

dialign2.2.1Segment-based multiple sequence alignment

dotter3.1Graphical dotplot program for detailed comparison of two sequences

ea-utils1.1.2+dfsgcommand-line tools for processing biological sequencing data

embassy-domainatrix0.1.650Extra EMBOSS commands to handle domain classification file

embassy-domalign0.1.650Extra EMBOSS commands for protein domain alignment

embassy-domsearch1:0.1.650Extra EMBOSS commands to search for protein domains

embassy-phylip3.69.650No description

emboss6.6.0+dfsgeuropean molecular biology open software suite

emboss-lib6.6.0+dfsgEMBOSS Libraries

estscan22.1detects coding regions of DNA sequences

exchanger1.0lets you store, annotate and share files via an omixed server

fasta36t2d5Collection of programs for searching DNA and protein databases.

fastdnaml1.2.2Tool for construction of phylogenetic trees of DNA sequences

fastqc0.11.3A quality control application for high throughput sequence data

fasttree2.1.7phylogenetic trees from alignments of nucleotide or protein sequences

fastx-toolkit0.0.14FASTQ/A short nucleotide reads pre-processing tools

fixups8.0Miscellanous fixups for Bio-Linux

fraggenescan1.19finds (fragmented) genes in short reads

galaxy-server1.bl.py27.20140730Web-based analysis environment for bioinformatics

galaxy-server-apache-proxy1.bl.py27.20140730Activates Apache2 proxy for Galaxy server, and PAM authentication

galaxy-server-pg-database1.bl.py27.20140730Activates PostgreSQL database back-end for Galaxy

galaxy-tools-bl1:0.5.1Standard set of tool wrappers for Galaxy server

gap2caf0.20100408Handles conversion of gap format assemblies to caf format.

geneious5.5.7Geneious Basic workbench from Biomatters

geneious-genbanksubmit1.3.0GenBank submission for Geneious workbench

genquery2.2.4GenQuery is a set of Perl libraries for managing SQL query templates and making web-based query forms.

glam21:4.10.0.1gapped protein motifs from unaligned sequences

glimmer33.02Gene detection in archea and bacteria

gnx-tools0.1+20120305Basic genome assembly statistic tool to calculate Nx values e.g. N50,N10,NG50

handlebar2.2.2Handlebar is a database for storing data about barcodes and acessing the data via a web front-end.

happy1.2Multipoint QTL Mapping in Genetically Heterogeneous Animals

hmmer3.1b1profile hidden Markov models for protein sequence analysis

hyphy2.1+20111219analysis of genetic sequences using multiple techniques

infernal1.1.1inference of RNA secondary structural alignments

isacreator1.6.0GUI to import and edit ISA dataset descriptions.

jaligner1.0+dfsgSmith-Waterman algorithm with Gotoh’s improvement

jalview2.8.0b1.dfsgmultiple alignment editor

jellyfish2.2.3count k-mers in DNA sequences

jemboss6.6.0+dfsggraphical user interface to EMBOSS

jmotu1.0.6Clusters barcode DNA sequence data into molecular operational taxonomic units

jprofilegrid2.0.5Multiple sequence alignment tool that generates ProfileGrids

keyring6Public key package for the Bio-Linux package repository

khmer1.1k-mer counting, filtering and graph traversal

khmer-example1.1k-mer counting, filtering and graph traversal

last-align393genome-scale comparison of biological sequences

lastz1.02.00Aligns two DNA sequences, inferring appropriate parameters automatically

libbiojava-java1:1.7.1Java API to biological data and applications (default version)

libbiojava-java-demos1:1.7.1Example programs for BioJava

libpandaseq-sam11.2~ppa0Pair-end read assembler

libpandaseq-url02.7~ppa0Pair-end read assembler — URL handler

libpandaseq52.7~ppa0Pair-end read assembler

lucy1.19pPreparation of raw DNA sequence fragments for sequence assembly

macs141.4.2.1Model-based Analysis of ChIP-Seq on short reads sequencers

mafft7.215Multiple alignment program for amino acid or nucleotide sequences

maq0.7.1maps short fixed-length polymorphic DNA sequence reads to reference sequences

maxd2.3.0maxd is a data warehouse and visualisation environment for genomic expression data.

mdust1:0.1+20020708repetitive sequence masker

meme1:4.10.0.1search for common motifs in DNA or protein sequences

mesquite2.74Software for evolutionary biology.

metavelvet1.2.02extension of Velvet assembler to de novo metagenomic assembly

microbiomeutil20101212+dfsgMicrobiome Analysis Utilities

mira-3rdparty20120706Additional useful tools to accomapany the MIRA assembler

mira-assembler4.9.5Whole Genome Shotgun and EST Sequence Assembler

mothur1.36.1+dfsgsequence analysis suite for research on microbiota

mothur-lookup-files1.pat lookup files for Mothur

mothur-mpi1.36.1+dfsgmpi-enabled binary for mothur

mrbayes-mpi3.2.2+dfsgBayesian Inference of Phylogeny – mpi version

msatfinder2.0.10Microsatellite Finder

mspcrunch2.5a BLAST post-processing filter.

mummer3.23~dfsgEfficient sequence alignment of full genomes

muscle1:3.8.31Multiple alignment program of protein sequences

mview1.51Multiple alignment viewer for sequence database search results.

natefoo-add-scores0.1+20101006small helper application used by Galaxy server

natefoo-taxonomy0.1+20101102small taxonomy applications used by Galaxy server

ncbi-blast+2.2.28next generation suite of BLAST sequence search tools

ncbi-blast+-legacy2.2.28NCBI Blast legacy call script

ncbi-seg0.0.20000620tool to mask segments of low compositional complexity in amino acid sequences

ncbi-tools-bin6.1.20120620NCBI libraries for biology applications (text-based utilities)

ncbi-tools-x116.1.20120620NCBI libraries for biology applications (X-based utilities)

njplot2.4phylogenetic tree drawing program

nrdb2Generates quasi-nonredundant protein and nucleotide sequence databases

ocount0.5Oligonucleotide frequency counter

oligoarray2.1Computes oligonucleotides for microarray construction

oligoarrayaux3.7Free software that is required for the OligoArray2.1 software.

omegamap0.5Detects natural selection and recombination in DNA or RNA sequences.

paml4.7Phylogenetic Analysis by Maximum Likelihood (PAML)

pandaseq2.7~ppa0Pair-end read assembler

pandaseq-dev2.7~ppa0Pair-end read assembler — Development tools

pandaseq-sam1.2~ppa0Pair-end read assembler

pandaseq-sam-dev1.2~ppa0Pair-end read assembler — Development tools

parafly0.0.2013.01.21parallel command processing using OpenMP

parsinsert1.04Parsimonious Insertion of unclassified sequences into phylogenetic trees

pass20.1+20101008Peak calling in ChIP data based on Poisson de-clumping

perm0.4.0Efficient mapping of short reads with periodic spaced seeds

pfaat1.0.034Sequence alignment editor designed for protein family analysis.

phylip1:3.695No description

phyml2:20120412Phylogenetic estimation using Maximum Likelihood

picard-tools1.105Command line tools to manipulate SAM and BAM files

plymouth-theme8.2Boot splash for Bio-Linux 8

prank0.0.140110Probabilistic Alignment Kit for DNA, codon and amino-acid sequences

predictprotein1.0.94suite of protein sequence analysis tools

priam2005.07Generate enzyme-specific profiles for metabolic pathyway prediction

primer32.3.6Tool to design flanking oligo nucleotides for DNA amplification

probcons1.12PROBabilistic CONSistency-based multiple sequence alignment

pymol1.7.2.1Molecular Graphics System

qiime1.9.1+dfsgQuantitative Insights Into Microbial Ecology

qiime-default-reference0.1.3QIIME default reference dataset

qtlcart1.17fMap quantitative traits using a map of molecular markers.

r-base3.2.2GNU R statistical computation and graphics system

r-base-core3.2.2GNU R core of statistical computation and graphics system

r-base-dev3.2.2GNU R installation of auxiliary GNU R packages

r-bioc-affy1.46.1GNU R package “Methods for Affymetrix Oligonucleotide

r-bioc-affyio1.36.0GNU R package “Tools for parsing Affymetrix data files”

r-bioc-annotate1.42.0GNU R package “Annotation for microarrays”

r-bioc-annotationdbi1.26.0GNU R package “Annotation Database Interface”

r-bioc-biobase2.28.0GNU R package “Biobase: Base functions for Bioconductor”

r-bioc-biocgenerics0.14.0GNU R package “S4 generic functions for Bioconductor”

r-bioc-biocinstaller1.18.4GNU R package “Install/Update Bioconductor and CRAN

r-bioc-biocparallel1.2.9GNU R package “Bioconductor facilities for parallel

r-bioc-biomart2.18.0GNU R Interface to BioMart databases (Ensembl, COSMIC, Wormbase and Gramene)

r-bioc-biostrings2.36.4GNU R package “String objects representing biological

r-bioc-bitseq1.8.0Bioconductor package “Transcript expression inference and differential

r-bioc-deseq1.16.0Differential gene expression analysis based on the -ve binomial distribn.

r-bioc-edger3.6.2GNU R package “Empirical analysis of digital gene

r-bioc-genefilter1.46.1GNU R package “genefilter: methods for filtering genes

r-bioc-geneplotter1.42.0Graphics related functions for Bioconductor

r-bioc-genomeinfodb1.4.2GNU R package “Utilities for manipulating chromosome and

r-bioc-genomicalignments1.4.1GNU R package “Representation and manipulation of short

r-bioc-genomicranges1.20.6GNU R package “Representation and manipulation of genomic

r-bioc-hilbertvis1.23.0GNU R package to visualise long vector data

r-bioc-impute1.38.1GNU R package “impute: Imputation for microarray data”

r-bioc-iranges2.2.7GNU R package “Infrastructure for manipulating intervals

r-bioc-limma3.20.5GNU R package “Linear Models for Microarray Data”

r-bioc-multtest2.24.0GNU R package “Resampling-based multiple hypothesis

r-bioc-pcamethods1.54.0Bioconductor “pcaMethods: A collection of PCA methods.”

r-bioc-preprocesscore1.30.0GNU R package “A collection of pre-processing functions”

r-bioc-qvalue1:1.38.0Bioconductor package “Q-value estimation for false discovery rate control”

r-bioc-rsamtools1.20.4GNU R package “Binary alignment (BAM), variant call (BCF),

r-bioc-s4vectors0.6.5GNU R package “S4 implementation of vectors and lists”

r-bioc-xvector0.8.0GNU R package “Representation and manpulation of external

r-bioc-zlibbioc1.10.0GNU R package “An R packaged zlib-1.2.5”

r-cran-abind1.4-0GNU R package “Combine multi-dimensional arrays”

r-cran-ade41.7-2GNU R package “Analysis of Ecological Data : Exploratory

r-cran-ape3.3GNU R package “Analyses of Phylogenetics and Evolution”

r-cran-aplpack1.3.0GNU R package “Another Plot PACKage: stem.leaf, bagplot,

r-cran-bitops1.0-6GNU R package implementing bitwise operations

r-cran-catools1.17.1GNU R package “Tools: moving window statistics, GIF,

r-cran-cluster2.0.3GNU R package for cluster analysis by Rousseeuw et al

r-cran-data.table1.9.4GNU R package “Extension of data.frame”

r-cran-dbi0.3.1GNU R package “R Database Interface”

r-cran-dichromat2.0.0Color schemes for dichromats

r-cran-digest0.6.8GNU R package “Create Cryptographic Hash Digests of R

r-cran-evaluate0.7.2GNU R package “Parsing and Evaluation Tools that Provide

r-cran-futile.logger1.4.1GNU R package “A Logging Utility for R”

r-cran-futile.options1.0.0GNU R package “Futile options management”

r-cran-gdata2.17.0GNU R package “Various R Programming Tools for Data

r-cran-gee4.13-19GNU R package “Generalized Estimation Equation Solver”

r-cran-getopt1.20.0GNU R package “C-like getopt behavior.”

r-cran-ggplot21.0.1GNU R package “An Implementation of the Grammar of

r-cran-gplots2.17.0GNU R package “Various R Programming Tools for Plotting

r-cran-gtable0.1.2GNU R package “Arrange grobs in tables.”

r-cran-gtools3.5.0GNU R package “Various R Programming Tools”

r-cran-labeling0.3GNU R package “Axis Labeling”

r-cran-lambda.r1.1.7GNU R package “Modeling Data with Functional Programming”

r-cran-lattice0.20-29GNU R package “Lattice Graphics”

r-cran-leaps2.9GNU R package “regression subset selection”

r-cran-lme41.1-9GNU R package for linear mixed effects model fitting

r-cran-locfit1.5-9.1Local Regression, Likelihood and Density Estimation.

r-cran-matrix1.2-2GNU R package of classes for dense and sparse matrices

r-cran-matrixstats0.10.0R package “Methods that apply to rows and columns of a matrix”

r-cran-munsell0.4.2GNU R package “Munsell colour system”

r-cran-nlme3.1.122GNU R package for (non-)linear mixed effects models

r-cran-optparse1.2.0GNU R package “Command line option parser.”

r-cran-permute0.8-4GNU R package “Functions for Generating Restricted

r-cran-plotrix3.5-7GNU R package “Various plotting functions”

r-cran-plyr1.8.3GNU R package “Tools for Splitting, Applying and Combining

r-cran-prettyr2.0-8GNU R package “Pretty descriptive stats.”

r-cran-propcis0.2-5GNU R package “PropCIs: Various confidence interval methods for proportions”

r-cran-proto0.3-10GNU R package “Prototype object-based programming”

r-cran-r.methodss31.6.1GNU R package “Utility function for defining S3 methods”

r-cran-rapidr0.1.1GNU R package “RAPIDR: Reliable Accurate Prenatal non-Invasive Diagnosis.”

r-cran-rcolorbrewer1.0-5GNU R package providing suitable color palettes

r-cran-rcpp0.12.1GNU R package “Seamless R and C++ Integration”

r-cran-rcurl1.95-4.7GNU R package “General Network (HTTP/FTP/…) Client

r-cran-relimp1.0-4GNU R package “Relative Contribution of Effects in a

r-cran-reshape21.4.1GNU R package “Flexibly Reshape Data: A Reboot of the

r-cran-rggobi2.1.20GNU R package for the GGobi data visualization system

r-cran-rgl0.95.1247GNU R package for three-dimensional visualisation using OpenGL

r-cran-rgtk22.20.31GNU R binding for Gtk2

r-cran-rmpi0.6-5GNU R package interfacing MPI libraries for distributed computing

r-cran-rserve1.7-3GNU R Rserve tcp/ip server and sample clients

r-cran-rsqlite1.0.0GNU R package “SQLite Interface for R”

r-cran-rwave2.4GNU R package “Time-Frequency Analysis of 1-D Signals”

r-cran-samr2.0GNU R package “SAM: Significance Analysis of Microarrays”

r-cran-scales0.3.0GNU R package “Scale Functions for Visualization”

r-cran-scatterplot3d0.3-36GNU R package “3D Scatter Plot”

r-cran-snowfall1.84-6GNU R package “Easier cluster computing (based on snow).”

r-cran-sp1:1.1-0GNU R package “Classes and Methods for Spatial Data”

r-cran-stringr1.0.0GNU R package “Simple, Consistent Wrappers for Common

r-cran-tcltk21.2-9GNU R package “Tcl/Tk Additions”

r-cran-testthat0.9.1GNU R package “Testthat code. Tools to make testing fun

r-cran-vegan2.3-0GNU R package “Community Ecology Package”

r-cran-waveslim1.7.5GNU R package “Basic wavelet routines for one-, two- and

r-cran-wavethresh4.6.6GNU R package “Wavelets statistics and transforms.”

r-cran-xml3.98-1.3GNU R package “Tools for Parsing and Generating XML Within

r-cran-xtable1:1.7-3GNU R coerce data to LaTeX and HTML tables

r-mathlib3.2.2GNU R standalone mathematics library

r-recommended3.2.2GNU R collection of recommended packages [metapackage]

rasmol2.7.5.2Visualize biological macromolecules

raxml8.0.26Randomized Axelerated Maximum Likelihood of phylogenetic trees

ray2.3.1parallel de novo genome assemblies of next-gen sequencing data

ray-extra2.3.1Scripts and XSL sheets for post-processing for ray de novo assembler

rbs-finder1.0A program to find Ribosomal binding sites.

rdp-classifier2.10.2+dfsgtaxonomic assignment from next generation sequencing

readseq1Conversion between sequence formats

rsem1.2.22+dfsgRNA-Seq by Expectation-Maximization

sampledata20041011Sample data for Bio-Linux packages

samtools0.1.19processing sequence alignments in SAM and BAM formats

scythe0.993Bayesian adapter trimmer for nextgen sequence reads

seaview1:4.4.2No description

seqprep1.1tool for stripping adaptors and/or merging paired reads with overlap

shared1.1Some shared files used by Bio-Linux

sickle1.33windowed adaptive trimming tool for FASTQ files using quality

sift4.0.3bpredicts if a substitution in a protein has a phenotypic effect

sortmerna2.0tool for filtering, mapping and OTU-picking NGS reads

splitstree4.12.6Analysis and visualisation tool for distance data from biological sequences

sputnik-mononucleotide0.1+20101005Searches DNA sequence files in FASTA format for microsatellite repeats

squint1.02Java-based multiple alignment program and editor

ssake3.8.1genomics application for assembling millions of very short DNA sequences

stacks1.34pipeline for building loci from short-read sequences

stacks-web1.34web interface for displaying loci from short-read sequences

staden2.0.0b10DNA sequence assembly (Gap4/Gap5), editing and analysis tools

staden-common2.0.0b10Architecture independent files for Staden

stars1.2aSTARS is an alternative interface to Staden.

sumatra1.0.01fast and exact comparison and clustering of sequences

swarm1.2.20robust and fast clustering method for amplicon-based studies

t-coffee10.00.r1613Multiple Sequence Alignment

tablet1.14.04.10Graphical viewer for next gen sequence assemblies and alignments

taxinspector1.0b3Browser for entries in the NCBI taxonomy database

tetra1.0b3tetranucleotide frequency calculator with GUI

themes-v77.0Graphics, icons, wallpaper and desktop settings for Bio-Linux 7

themes-v88.0Graphics, icons, wallpaper and desktop settings for Bio-Linux 8

tophat2.1.0fast splice junction mapper for RNA-Seq reads

trace2dbest3.14Processes trace files into dbEST submissions

transdecoder2.0.1+dfsgfind coding regions within transcripts

transterm-hp2.07Transterm finds rho-independent transcription terminators in bacterial genomes.

transtermhp2.09find rho-independent transcription terminators in bacterial genomes

tree-puzzle5.2Reconstruction of phylogenetic trees by maximum likelihood

tree-puzzle-doc5.2Reconstruction of phylogenetic trees by maximum likelihood

treeviewx0.5.1+20100823Displays and prints phylogenetic trees

trinityrnaseq2.0.6+dfsgRNA-Seq De novo Assembly

trinityrnaseq-sampledata2.0.6+dfsgRNA-Seq De novo Assembly

trnascan1.23tRNAscan-SE searches for tRNA genes in genomic sequences.

trnascan-se1.3.1search for tRNA genes in genomic sequences

tutorials1Tutorials and documentation for Bio-Linux users.

ugene1.18.0+repackintegrated bioinformatics toolkit

unity-lens0.2unity lens for Bio-Linux

usb-maker8.2Script to generate Bio-Linux live memory sticks.

velvet1.2.10+dfsgNucleic acid sequence assembler for very short reads

velvet-example1.2.10+dfsgExample data for the Velvet sequence assembler

velvet-long1.2.10+dfsgNucleic acid sequence assembler for very short reads, long version

velvetoptimiser2.2.5Automatically optimise Velvet do novo assembly parameters

vsearch1.1.1.nodatatool for processing metagenomic sequences

weblogo3.3create sequence logos from biological sequence alignments

wise2.4.1comparison of biopolymers, commonly DNA and protein sequences

xcut1.4.2A re-write of the GNU cut command with many new features.

zsh1Z-Shell wrapper package for Bio-Linux.