| Tools & Software | Description |
|---|
| ABySS 1.3.5 | de novo, parallel, sequence assembler for short reads |
| ampliconnoise 1.28 | Programs for the removal of noise from 454 sequenced PCR amplicons |
| arb 5.5 | Integrated package for sequence database handling and analysis |
| archaeopteryx 0.972.beta9M | A phylogenetic tree viewer and editor |
| artemis 13.2 | Free genome viewer and annotation tool |
| assembly-conversion-tools 0.01 | Conversion tools for handling 454 assemblies. |
| backups 0.3 | Bio-Linux 5/6 backup utilities. |
| beam2 0.1+20101008 | SNP-SNP interaction association mapping based on SNP-block models |
| bedtools 2.17.0 | suite of utilities for comparing genomic features |
| big-blast 1.0.3 | The big-blast script for annotation of long sequences |
| biocode 2.3.3 | Biocode plugin for Geneious workbench |
| bioperl 1.6.901 | Perl tools for computational molecular biology |
| bioperl-run 1.6.9 | BioPerl wrappers: scripts |
| biosquid 1.9g+cvs20050121 | utilities for biological sequence analysis |
| bitseq 0.4.3 | Bayesian Inference of Transcripts from Sequencing Data |
| blast2 1:2.2.25.20110713 | Basic Local Alignment Search Tool |
| bldp-files 1.1 | Documentation for bioinformatics software on Bio-Linux. |
| blimps-utils 3.9 | blocks database improved searcher |
| blixem 3.1.1 | Interactive browser for viewing pairwise Blast results. |
| bowtie 1.0.0-1 | ultrafast memory-efficient short read aligner |
| bowtie2 2.1.0-1 | ultrafast memory-efficient short read aligner |
| bwa 0.6.1 | Burrows-Wheeler Aligner |
| cap3 20080520 | A base calling system |
| catchall 3.0.1 catchall 3.0.1 | Analyze data about microbial species abundance |
| cd-hit 4.6.1-2012-08-27 | suite of programs designed to quickly group sequences |
| cdbfasta 20100722 | Constant DataBase indexing and retrieval tools for multi-FASTA files |
| chimeraslayer 20101212 | detects likely chimeras in PCR amplified DNA |
| clc sequence viewer 6.4 | CLC Free Sequence Viewer |
| clustalw 2.1+lgpl | global multiple nucleotide or peptide sequence alignment |
| clustalx 2.1+lgpl | CLUSTAL X is a new windows interface for the widely-used progressive multiple sequence alignment program CLUSTAL W |
| cortex-con 0.05 | efficient and low-memory software for consensus genome assembly |
| cufflinks 2.1.1 | Transcript assembly, differential expression and regulation for RNA-Seq |
| cytoscape 1.2.7.0 | Platform for visualizing complex-networks and integrating these with attribute data |
| cytoscape 1.4.0 | Interactive viewer for large phylogenetic trees. |
| dialign 2.2.1 | Segment-based multiple sequence alignment |
| dotter 3.1 | Graphical dotplot program for detailed comparison of two sequences |
| embassy-domainatrix 0.1.650 | Extra EMBOSS commands to handle domain classification file |
| embassy-domalign 0.1.650 | Extra EMBOSS commands for protein domain alignment |
| embassy-domsearch 1:0.1.650 | Extra EMBOSS commands to search for protein domains |
| embassy-phylip 3.69.650 | EMBOSS conversions of the programs in the phylip package |
| emboss 6.5.7 | european molecular biology open software suite |
| emboss-lib 6.5.7 | EMBOSS Libraries |
| estscan2 2.1 | detects coding regions of DNA sequences |
| exchanger 1 | annotate and share files via an omixed server |
| fasta 36t2d5 | Collection of programs for searching DNA and protein databases. |
| fastdnaml 1.2.2 | Tool for construction of phylogenetic trees of DNA sequences |
| fastqc 0.10.1 | A quality control application for high throughput sequence data |
| fasttree 2.1.3 | Infers approximately-maximum-likelihood phylogenetic trees |
| fastx-toolkit 0.0.13.1 | FASTQ/A short nucleotide reads pre-processing tools |
| galaxy-server 1.bl.py27.20120718 | A web-based analysis environment |
| gap2caf 0.20100408 | Handles conversion of gap format assemblies to caf format. |
| geneious 5.5.7 | Geneious Basic workbench from Biomatters |
| geneious-genbanksubmit 1.3.0 | GenBank submission for Geneious workbench |
| genquery 2.2.4 | GenQuery is a set of Perl libraries for managing SQL query templates and making web-based query forms. |
| glam2 4.8.1 | gapped protein motifs from unaligned sequences |
| glimmer3 3.02 | System for finding genes in microbial DNA. |
| gnx-tools 0.1+20120305 | Basic genome assembly statistic tool to calculate Nx values e.g. N50,N10,NG50 |
| handlebar 2.2.2 | Handlebar is a database for storing data about barcodes and acessing the data via a web front-end. |
| happy 1.2 | Multipoint QTL Mapping in Genetically Heterogeneous Animals |
| hmmer 3.1b1 | profile hidden Markov models for protein sequence analysis |
| hmmer2 2.3.2 | profile hidden Markov models for protein sequence analysis |
| hmmer2-pvm 2.3.2 | HMMER programs with PVM (Parallel Virtual Machine) support |
| hyphy 2.1+20111219 | analysis of genetic sequences using multiple techniques |
| infernal 1.0.2 | inference of RNA secondary structural alignments |
| io-lib-tools 1.13.1 | command line tools provided with Staden io-lib |
| isacreator 1.6.0 | GUI to import and edit ISA dataset descriptions. |
| jalview 1:2.7.0 | a Java multiple alignment editor |
| jalview 1:2.7.0 | count k-mers in DNA sequences |
| jemboss 6.5.7 | graphical user interface to EMBOSS |
| jmotu 1.0.6 | Clusters barcode DNA sequence data into molecular operational taxonomic units |
| jprofilegrid 2.0.5 | Multiple sequence alignment tool that generates ProfileGrids |
| keyring 5 | Public key package for the Bio-Linux package repository |
| last-align 189 | genome-scale comparison of biological sequences |
| lastz 1.02.00 | Aligns two DNA sequences, inferring appropriate parameters automatically |
| libbiojava-java 1:1.7.1 | Java API to biological data and applications |
| libbiojava-java-demos 1:1.7.1 | Example programs for BioJava |
| lucy 1.19p | Preparation of raw DNA sequence fragments for sequence assembly |
| macs 2.0.9.1 | Model-based Analysis of ChIP-Seq on short reads sequencers |
| macs 2.0.9.1 | Model-based Analysis of ChIP-Seq on short reads sequencers |
| mafft 7.037 | Multiple alignment program for amino acid or nucleotide sequences |
| maq 0.7.1 | maps short fixed-length polymorphic DNA sequence reads to reference sequences |
| maxd 2.3.0 | maxd is a data warehouse and visualisation environment for genomic expression data. |
| mdust 1:0.1+20020708 | repetitive sequence masker |
| meme 4.8.1 | search for common motifs in DNA or protein sequences |
| mesquite 2.74 | Software for evolutionary biology. |
| microbiomeutil 20101212 | Microbiome Analysis Utilities |
| mira-3rdparty 20120706 | Additional useful tools to accomapany the MIRA assembler |
| mira-assembler 3.4.1.1 | Whole Genome Shotgun and EST Sequence Assembler |
| mothur 1.30.2+repack | sequence analysis suite for research on microbiota |
| mothur-mpi 1.30.2+repack | mpi-enabled binary for mothur |
| mrbayes 3.2.1+dfsg+repack | Bayesian Inference of Phylogeny |
| mrbayes-mpi 3.2.1+dfsg+repack | Bayesian Inference of Phylogeny - mpi version |
| msatfinder 2.0.10 | Microsatellite Finder |
| mspcrunch 2.5 | a BLAST post-processing filter. |
| mummer 3.23~dfsg | Efficient sequence alignment of full genomes |
| muscle 1:3.8.31 | Multiple alignment program of protein sequences |
| mview 1.51 | Multiple alignment viewer for sequence database search results. |
| nast-ier 20101212 | NAST-based DNA alignment tool |
| natefoo-add-scores 0.1+20101006 | small helper application used by Galaxy server |
| natefoo-taxonomy 0.1+20101102 | small taxonomy applications used by Galaxy server |
| ncbi-blast+ 2.2.28 | next generation suite of BLAST sequence search tools |
| ncbi-blast+-legacy 2.2.28 | NCBI Blast legacy call script |
| ncbi-blast+-static 2.2.26 | next generation suite of BLAST sequence search tools |
| ncbi-seg 0.0.20000620 | tool to mask segments of low compositional complexity in amino acid sequences |
| ncbi-tools-bin 6.1.20110713 | NCBI libraries for biology applications (text-based utilities) |
| ncbi-tools-x11 6.1.20110713 | NCBI libraries for biology applications (X-based utilities) |
| njplot 2.3 | phylogenetic tree drawing program |
| norsnet 1.0.16 | tool to identify unstructured loops in proteins |
| norsp 1.0.5 | predictor of non-regular secondary structure |
| nrdb 2 | Generates quasi-nonredundant protein and nucleotide sequence databases. |
| ocount 0.5 | Oligonucleotide frequency counter |
| oligoarray 2.1 | Computes oligonucleotides for microarray construction |
| oligoarrayaux 3.7 | Free software that is required for the OligoArray2.1 software. |
| omegamap 0.5 | Detects natural selection and recombination in DNA or RNA sequences. |
| paml 4.5 | Phylogenetic Analysis by Maximum Likelihood (PAML) |
| pass2 0.1+20101008 | Peak calling in ChIP data based on Poisson de-clumping |
| perm 0.3.9 | Efficient mapping of short reads with periodic spaced seeds |
| pfaat 1.0.034 | Sequence alignment editor designed for protein family analysis. |
| phylip 01:03.7 | package of programs for inferring phylogenies |
| phyml 2:20110919 | Phylogenetic estimation using Maximum Likelihood |
| picard-tools 1.91 | Command line tools to manipulate SAM and BAM files |
| plymouth-theme 7 | Boot splash for Bio-Linux 7 |
| prank 0.0.120716 | Probabilistic Alignment Kit for DNA, codon and amino-acid sequences |
| predictnls 1.0.20 | prediction and analysis of protein nuclear localization signals |
| predictprotein 1.0.86 | suite of protein sequence analysis tools |
| primer3 2.2.3 | Tool to design flanking oligo nucleotides for DNA amplification |
| probcons 1.12 | PROBabilistic CONSistency-based multiple sequence alignment |
| profbval 1.0.22 | predictor of flexible/rigid protein residues from sequence |
| profisis 1.0.11 | prediction of protein-protein interaction sites from sequence |
| profphd 1.0.39 | secondary structure and solvent accessibility predictor |
| proftmb 1.1.10 | per-residue prediction of bacterial transmembrane beta barrels |
| qiime 1.7.0 | Quantitative Insights Into Microbial Ecology |
| r-base 3.0.1 | GNU R statistical computation and graphics system |
| r-base-core 3.0.1 | GNU R core of statistical computation and graphics system |
| r-base-dev 3.0.1 | GNU R installation of auxiliary GNU R packages |
| r-bioc-affy 1.38.1 | GNU R package "Methods for Affymetrix Oligonucleotide |
| r-bioc-affyio 1.28.0 | GNU R package "Tools for parsing Affymetrix data files" |
| r-bioc-annotationdbi 1.22.2 | GNU R package "Annotation Database Interface" |
| r-bioc-biobase 2.20.0 | GNU R package "Biobase: Base functions for Bioconductor" |
| r-bioc-biocgenerics 0.6.0 | GNU R package "Generic functions for Bioconductor" |
| r-bioc-biocinstaller 1.10.0 | GNU R package "Install/Update Bioconductor and CRAN |
| r-bioc-biomart 2.16.0 | GNU R package "Interface to BioMart databases (e.g. |
| r-bioc-biostrings 2.28.0 | GNU R package "String objects representing biological |
| r-bioc-bitseq 1.4.2 | Bioconductor package "Transcript expression inference and differential |
| r-bioc-edger 3.2.3 | GNU R package "Empirical analysis of digital gene |
| r-bioc-genomicranges 1.12.2 | GNU R package "Representation and manipulation of genomic |
| r-bioc-hilbertvis 1.19.0 | GNU R package to visualise long vector data |
| r-bioc-impute 1.34.0 | GNU R package "impute: Imputation for microarray data" |
| r-bioc-iranges 1.18.0 | GNU R package "Infrastructure for manipulating intervals |
| r-bioc-limma 3.16.1 | GNU R package "Linear Models for Microarray Data" |
| r-bioc-multtest 2.16.0 | GNU R package "Resampling-based multiple hypothesis |
| r-bioc-pcamethods 1.50.0 | Bioconductor "pcaMethods: A collection of PCA methods." |
| r-bioc-preprocesscore 1.22.0 | GNU R package "A collection of pre-processing functions" |
| r-bioc-qvalue 1:1.34.0 | Bioconductor package "Q-value estimation for false discovery rate control" |
| r-bioc-rsamtools 1.12.2 | GNU R package "Binary alignment (BAM), variant call (BCF), |
| r-bioc-zlibbioc 1.6.0 | GNU R package "An R packaged zlib-1.2.5" |
| r-cran-abind 1.4-0 | GNU R package "Combine multi-dimensional arrays" |
| r-cran-ade4 1.5-2 | GNU R package "Analysis of Ecological Data : Exploratory |
| r-cran-ape 3.0-8 | GNU R package "Analyses of Phylogenetics and Evolution" |
| r-cran-aplpack 1.2.7 | GNU R package "Another Plot PACKage: stem.leaf, bagplot, |
| r-cran-bitops 1.0-5 | GNU R package "Bitwise Operations" |
| r-cran-catools 1.14 | GNU R package "Tools: moving window statistics, GIF, |
| r-cran-cluster 1.14.4 | GNU R package for cluster analysis by Rousseeuw et al |
| r-cran-dbi 0.2-6 | GNU R package providing a generic database interface |
| r-cran-digest 0.6.3 | GNU R package "Create cryptographic hash digests of R objects" |
| r-cran-evaluate 0.4.3 | GNU R package "Parsing and evaluation tools that provide |
| r-cran-gdata 2.12.0.2 | GNU R package with data manipulation tools by Greg Warnes et al |
| r-cran-gee 4.13r18 | GNU R package "Generalized Estimation Equation solver" |
| r-cran-gplots 2.11.0.1 | GNU R package with tools for plotting data by Greg Warnes et al |
| r-cran-gtools 2.7.1 | GNU R package with R programming tools by Greg Warnes et al |
| r-cran-lattice 0.20-15 | GNU R package "Lattice Graphics" |
| r-cran-leaps 2.9 | GNU R package "regression subset selection" |
| r-cran-lme4 0.999999-2 | GNU R package for linear mixed effects model fitting |
| r-cran-matrix 1.0-12 | GNU R package of classes for dense and sparse matrices |
| r-cran-matrixstats 0.8.1 | R package "Methods that apply to rows and columns of a matrix" |
| r-cran-nlme 3.1.109 | GNU R package for (non-)linear mixed effects models |
| r-cran-permute 0.7-0 | R functions for generating restricted permutations of data |
| r-cran-plotrix 3.4-7 | GNU R package providing various plotting functions |
| r-cran-prettyr 2.0-7 | GNU R package "Pretty descriptive stats." |
| r-cran-qvalue 1.26.0 | GNU R package "Q-value estimation for false discovery rate |
| r-cran-r.methodss3 1.4.2 | GNU R package "Utility function for defining S3 methods" |
| r-cran-rcpp 0.10.3 | GNU R package "Seamless R and C++ Integration" |
| r-cran-rcurl 1.95-4.1 | RCurl: General network (HTTP/FTP/...) client interface for R |
| r-cran-relimp 1.0-3 | GNU R package for inference on relative importance of regressors |
| r-cran-rggobi 2.1.19 | GNU R package for the GGobi data visualization system |
| r-cran-rgl 0.93.935 | GNU R package for three-dimensional visualisation using OpenGL |
| r-cran-rgtk2 2.20.25 | GNU R binding for Gtk2 |
| r-cran-rsqlite 0.11.3 | GNU R package "SQLite interface for R" |
| r-cran-rwave 2.1 | GNU R package "Time-Frequency analysis of 1-D signals" |
| r-cran-samr 2 | GNU R package "SAM: Significance Analysis of Microarrays" |
| r-cran-scatterplot3d 0.3-33 | GNU R package for Visualizing Multivariate Data |
| r-cran-sp 1:1.0-9 | GNU R classes and methods for spatial data |
| r-cran-stringr 0.6.2 | GNU R package "Make it easier to work with strings." |
| r-cran-tcltk2 1.2.5 | GNU R package "Tcl/Tk Additions" |
| r-cran-testthat 0.7.1 | GNU R package "Testthat code. Tools to make testing fun :)" |
| r-cran-vegan 2.0-7 | Community Ecology Package for R |
| r-cran-waveslim 1.7.1 | GNU R package "Basic wavelet routines for one-, two- and |
| r-cran-wavethresh 4.6.2 | GNU R package "Wavelets statistics and transforms." |
| r-cran-xml | GNU R package "Tools for parsing and generating XML within |
| r-cran-xtable 1:1.7-1 | GNU R coerce data to LaTeX and HTML tables |
| r-mathlib 3.0.1 | GNU R standalone mathematics library |
| r-recommended 3.0.1 | GNU R collection of recommended packages [metapackage] |
| rasmol 2.7.5 | Randomized Axelerated Maximum Likelihood of phylogenetic trees |
| ray 2.2.0 | parallel genome assemblies for parallel DNA sequencing |
| rbs-finder 1 | A program to find Ribosomal binding sites. |
| rdp-classifier 2.5+repack | taxonomic assignment from next generation sequencing |
| readseq 1 | Conversion between sequence formats |
| samtools 0.1.18 | processing sequence alignments in SAM and BAM formats |
| scythe 0.991 | Bayesian adapter trimmer for nextgen sequence reads |
| seaview 1:4.3.1 | Multiplatform interface for sequence alignment and phylogeny |
| seqan-apps 1.3.1 | C++ library for the analysis of biological sequences |
| sickle 0.94 | windowed adaptive trimming tool for FASTQ files using quality |
| sift 4.0.3b | predicts if a substitution in a protein has a phenotypic effect |
| splitstree 4.13.1 | Analysis and visualisation tool for distance data from biological sequences |
| sputnik-mononucleotide 0.1+20101005 | Searches dna sequence files in Fasta format for microsatellite repeat. |
| squint 1.02 | Java-based multiple alignment program and editor |
| ssake 3.8 | genomics application for assembling millions of very short DNA sequences |
| staden 2006.1.7.0+1.11.6 | A suite of tools for sequence analysis. |
| staden-io-lib-utils 1.13.1 | programs for maniuplating DNA sequencing files |
| stars 1.2a | STARS is an alternative interface to Staden. |
| t-coffee 9.03.r1318 | Multiple Sequence Alignment |
| tablet 1.12.03.26 | Graphical viewer for next gen sequence assemblies and alignments |
| taverna 1.7 | Workflow tool that make use of web services. |
| taxinspector 1.0b3 | Browser for entries in the NCBI taxonomy database |
| tetra 1.0b3 | tetranucleotide frequency calculator with GUI |
| tigr-glimmer 3.02 | Gene detection in archea and bacteria |
| tophat 2.0.8 | fast splice junction mapper for RNA-Seq reads |
| trace2dbest 3.14 | Processes trace files into dbEST submissions |
| transterm-hp 2.07 | Transterm finds rho-independent transcription terminators in bacterial genomes. |
| transtermhp 2.09 | find rho-independent transcription terminators in bacterial genomes |
| tree-puzzle 5.2 | Reconstruction of phylogenetic trees by maximum likelihood |
| tree-puzzle-doc 5.2 | Reconstruction of phylogenetic trees by maximum likelihood |
| treeviewx 0.5.1+20100823 | Displays and prints phylogenetic trees |
| trnascan 1.21 | tRNAscan-SE searches for tRNA genes in genomic sequences. |
| trnascan-se 1.3.1 | search for tRNA genes in genomic sequences |
| ugene 1.9.8+repack | integrated bioinformatics toolkit |
| velvet 1.2.08 | Nucleic acid sequence assembler for very short reads |
| velvet 1.2.08 | Example data for the Velvet sequence assembler |
| velvet-long 1.2.08 | Nucleic acid sequence assembler for very short reads, long version |
| velvet-long 1.2.08 | A tool for creating sequence logos from biological sequence alignments |
| wigeon 20101212 | reimplementation of the Pintail 16S DNA anomaly detection utility |
| wise 2.4.1 | comparison of biopolymers, commonly DNA and protein sequences |
| zsh 1 | Z-Shell wrapper package for Bio-Linux. |
| ClustalX 2.0, | Interactive program for multiple sequence alignment. Friendly GUI. |
| Cn3D | Structure visualizer for NCBI's Entrez retrieval service. |
| EMBOSS tools | A suite of program for sequence and pattern alignment, protein motif identification and more. |
| Garlic | Interactive program for molecular visualization. Friendly GUI. |
| Glimmer | Glimmer is a system for finding genes in microbial DNA, especially the genomes of bacteria, archaea, and viruses. |
| Gromacs | Suite of programs for molecular dynamics and more. |
| GP/Arka | Programs for manipulation of DNA/RNA/protein sequences. |
| NCBI Toolkit | Bioinformatics tools from NCBI. |
| NJPlot | A binary tree drawing program for phylogenetic trees. |
| PyMOL | Molecular visualization program with high quality image output. |
| Ramachandran Plot Explorer | Protein visualizer |
| Rasmol | Molecular visualization program |
| Raster3D | Program for high quality image output for biomolecules. |
| SeaView | SeaView is a graphical multiple sequence alignment. |
| TINKER | Software tools for molecular modeling (MD). |
| Accelrys/Accord | Structure viewing / management / File format conversion |
| Open Babel | Converts between different file formats for computational biology applications |
