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.
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