Bio-Linux Software List

Software on Bio-Linux 8

The bioinfomatics software on Bio-Linux consists of the packages below, which includes our own packages as well as bioinformatics packages from the main Debian and Ubuntu repositories. This list was last updated in September 2015 and new and updated packages may have been added since then.

Most of these packages work from the command line, so just type the name of the program to run it, or for R packages activate them using the “library(…)” function.  To get more info on a package type “dpkg -s packagename” or to see the local docs for a package type “go /usr/share/doc/packagename“. GUI applications can be located through the Installed Applications section of the main Dash menu (the button in the top left corner of the screen).


Package Version Description
abyss 1.9.0 de novo, parallel, sequence assembler for short reads
ampliconnoise 1.29 Programs for the removal of noise from 454 sequenced PCR amplicons
arb 5.5 No description
archaeopteryx 0.972.beta9M A phylogenetic tree viewer and editor
artemis 16.0.0 Free genome viewer and annotation tool
assembly-conversion-tools 0.01 Conversion tools for handling 454 assemblies.
axiome 1.7biolinux1 QIIME and mothur automation toolkit
axiome-dev 1.7biolinux1 QIIME automation toolkit — Plugin Development
backups 0.3 Bio-Linux 5/6/7 backup utilities.
bamtools 2.4.0+dfsg toolkit for manipulating BAM (genome alignment) files
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
berkeley-express 1.5.1 Streaming quantification for high-throughput sequencing
big-blast 1.0.3 The big-blast script for annotation of long sequences
biocode 2.3.3 Biocode plugin for Geneious workbench
bioperl 1.6.923 Perl tools for computational molecular biology
bioperl-run 1.6.9 BioPerl wrappers: scripts
biosquid 1.9g+cvs20050121 utilities for biological sequence analysis
bitseq 0.7.0 Bayesian Inference of Transcripts from Sequencing Data
blast2 1: 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 1.1.1 Ultrafast memory-efficient short read aligner
bowtie2 2.2.6 ultrafast memory-efficient short read aligner
bowtie2-debug 2.2.6 ultrafast memory-efficient short read aligner
bwa 0.7.12 Burrows-Wheeler Aligner
cap3 20080520 A base calling system
catchall 3.0.1 Analyze data about microbial species abundance
cd-hit 2009-1020 a suite of programs designed to quickly group sequences
cdbfasta 20100722 Constant DataBase indexing and retrieval tools for multi-FASTA files
chimeraslayer 20101212+dfsg detects likely chimeras in PCR amplified DNA
clcsequenceviewer 6.4 CLC Free Sequence Viewer
clearcut 1.0.9 Relaxed Neighbor Joining
clustalw 2.1+lgpl No description
clustalx 2.1+lgpl No description
cortex-con 0.05 efficient and low-memory software for consensus genome assembly
cruft-killer 0.3 Remove cruft from Bio-Linux desktop
cufflinks 2.2.1 Transcript assembly, differential expression and regulation for RNA-Seq
cytoscape 1:3.2.1 Platform for visualizing complex-networks and integrating these with attribute data
dendroscope 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
ea-utils 1.1.2+dfsg command-line tools for processing biological sequencing data
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 No description
emboss 6.6.0+dfsg european molecular biology open software suite
emboss-lib 6.6.0+dfsg EMBOSS Libraries
estscan2 2.1 detects coding regions of DNA sequences
exchanger 1.0 lets you store, 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 0.11.3 A quality control application for high throughput sequence data
fasttree 2.1.7 phylogenetic trees from alignments of nucleotide or protein sequences
fastx-toolkit 0.0.14 FASTQ/A short nucleotide reads pre-processing tools
fixups 8.0 Miscellanous fixups for Bio-Linux
fraggenescan 1.19 finds (fragmented) genes in short reads
galaxy-server 1.bl.py27.20140730 Web-based analysis environment for bioinformatics
galaxy-server-apache-proxy 1.bl.py27.20140730 Activates Apache2 proxy for Galaxy server, and PAM authentication
galaxy-server-pg-database 1.bl.py27.20140730 Activates PostgreSQL database back-end for Galaxy
galaxy-tools-bl 1:0.5.1 Standard set of tool wrappers for Galaxy server
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 1: gapped protein motifs from unaligned sequences
glimmer3 3.02 Gene detection in archea and bacteria
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
hyphy 2.1+20111219 analysis of genetic sequences using multiple techniques
infernal 1.1.1 inference of RNA secondary structural alignments
isacreator 1.6.0 GUI to import and edit ISA dataset descriptions.
jaligner 1.0+dfsg Smith-Waterman algorithm with Gotoh’s improvement
jalview 2.8.0b1.dfsg multiple alignment editor
jellyfish 2.2.3 count k-mers in DNA sequences
jemboss 6.6.0+dfsg 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 6 Public key package for the Bio-Linux package repository
khmer 1.1 k-mer counting, filtering and graph traversal
khmer-example 1.1 k-mer counting, filtering and graph traversal
last-align 393 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 (default version)
libbiojava-java-demos 1:1.7.1 Example programs for BioJava
libpandaseq-sam1 1.2~ppa0 Pair-end read assembler
libpandaseq-url0 2.7~ppa0 Pair-end read assembler — URL handler
libpandaseq5 2.7~ppa0 Pair-end read assembler
lucy 1.19p Preparation of raw DNA sequence fragments for sequence assembly
macs14 Model-based Analysis of ChIP-Seq on short reads sequencers
mafft 7.215 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 1: search for common motifs in DNA or protein sequences
mesquite 2.74 Software for evolutionary biology.
metavelvet 1.2.02 extension of Velvet assembler to de novo metagenomic assembly
microbiomeutil 20101212+dfsg Microbiome Analysis Utilities
mira-3rdparty 20120706 Additional useful tools to accomapany the MIRA assembler
mira-assembler 4.9.5 Whole Genome Shotgun and EST Sequence Assembler
mothur 1.36.1+dfsg sequence analysis suite for research on microbiota
mothur-lookup-files 1 .pat lookup files for Mothur
mothur-mpi 1.36.1+dfsg mpi-enabled binary for mothur
mrbayes-mpi 3.2.2+dfsg 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.
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-seg 0.0.20000620 tool to mask segments of low compositional complexity in amino acid sequences
ncbi-tools-bin 6.1.20120620 NCBI libraries for biology applications (text-based utilities)
ncbi-tools-x11 6.1.20120620 NCBI libraries for biology applications (X-based utilities)
njplot 2.4 phylogenetic tree drawing program
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 4.7 Phylogenetic Analysis by Maximum Likelihood (PAML)
pandaseq 2.7~ppa0 Pair-end read assembler
pandaseq-dev 2.7~ppa0 Pair-end read assembler — Development tools
pandaseq-sam 1.2~ppa0 Pair-end read assembler
pandaseq-sam-dev 1.2~ppa0 Pair-end read assembler — Development tools
parafly 0.0.2013.01.21 parallel command processing using OpenMP
parsinsert 1.04 Parsimonious Insertion of unclassified sequences into phylogenetic trees
pass2 0.1+20101008 Peak calling in ChIP data based on Poisson de-clumping
perm 0.4.0 Efficient mapping of short reads with periodic spaced seeds
pfaat 1.0.034 Sequence alignment editor designed for protein family analysis.
phylip 1:3.695 No description
phyml 2:20120412 Phylogenetic estimation using Maximum Likelihood
picard-tools 1.105 Command line tools to manipulate SAM and BAM files
plymouth-theme 8.2 Boot splash for Bio-Linux 8
prank 0.0.140110 Probabilistic Alignment Kit for DNA, codon and amino-acid sequences
predictprotein 1.0.94 suite of protein sequence analysis tools
priam 2005.07 Generate enzyme-specific profiles for metabolic pathyway prediction
primer3 2.3.6 Tool to design flanking oligo nucleotides for DNA amplification
probcons 1.12 PROBabilistic CONSistency-based multiple sequence alignment
pymol Molecular Graphics System
qiime 1.9.1+dfsg Quantitative Insights Into Microbial Ecology
qiime-default-reference 0.1.3 QIIME default reference dataset
qtlcart 1.17f Map quantitative traits using a map of molecular markers.
r-base 3.2.2 GNU R statistical computation and graphics system
r-base-core 3.2.2 GNU R core of statistical computation and graphics system
r-base-dev 3.2.2 GNU R installation of auxiliary GNU R packages
r-bioc-affy 1.46.1 GNU R package “Methods for Affymetrix Oligonucleotide
r-bioc-affyio 1.36.0 GNU R package “Tools for parsing Affymetrix data files”
r-bioc-annotate 1.42.0 GNU R package “Annotation for microarrays”
r-bioc-annotationdbi 1.26.0 GNU R package “Annotation Database Interface”
r-bioc-biobase 2.28.0 GNU R package “Biobase: Base functions for Bioconductor”
r-bioc-biocgenerics 0.14.0 GNU R package “S4 generic functions for Bioconductor”
r-bioc-biocinstaller 1.18.4 GNU R package “Install/Update Bioconductor and CRAN
r-bioc-biocparallel 1.2.9 GNU R package “Bioconductor facilities for parallel
r-bioc-biomart 2.18.0 GNU R Interface to BioMart databases (Ensembl, COSMIC, Wormbase and Gramene)
r-bioc-biostrings 2.36.4 GNU R package “String objects representing biological
r-bioc-bitseq 1.8.0 Bioconductor package “Transcript expression inference and differential
r-bioc-deseq 1.16.0 Differential gene expression analysis based on the -ve binomial distribn.
r-bioc-edger 3.6.2 GNU R package “Empirical analysis of digital gene
r-bioc-genefilter 1.46.1 GNU R package “genefilter: methods for filtering genes
r-bioc-geneplotter 1.42.0 Graphics related functions for Bioconductor
r-bioc-genomeinfodb 1.4.2 GNU R package “Utilities for manipulating chromosome and
r-bioc-genomicalignments 1.4.1 GNU R package “Representation and manipulation of short
r-bioc-genomicranges 1.20.6 GNU R package “Representation and manipulation of genomic
r-bioc-hilbertvis 1.23.0 GNU R package to visualise long vector data
r-bioc-impute 1.38.1 GNU R package “impute: Imputation for microarray data”
r-bioc-iranges 2.2.7 GNU R package “Infrastructure for manipulating intervals
r-bioc-limma 3.20.5 GNU R package “Linear Models for Microarray Data”
r-bioc-multtest 2.24.0 GNU R package “Resampling-based multiple hypothesis
r-bioc-pcamethods 1.54.0 Bioconductor “pcaMethods: A collection of PCA methods.”
r-bioc-preprocesscore 1.30.0 GNU R package “A collection of pre-processing functions”
r-bioc-qvalue 1:1.38.0 Bioconductor package “Q-value estimation for false discovery rate control”
r-bioc-rsamtools 1.20.4 GNU R package “Binary alignment (BAM), variant call (BCF),
r-bioc-s4vectors 0.6.5 GNU R package “S4 implementation of vectors and lists”
r-bioc-xvector 0.8.0 GNU R package “Representation and manpulation of external
r-bioc-zlibbioc 1.10.0 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 1.7-2 GNU R package “Analysis of Ecological Data : Exploratory
r-cran-ape 3.3 GNU R package “Analyses of Phylogenetics and Evolution”
r-cran-aplpack 1.3.0 GNU R package “Another Plot PACKage: stem.leaf, bagplot,
r-cran-bitops 1.0-6 GNU R package implementing bitwise operations
r-cran-catools 1.17.1 GNU R package “Tools: moving window statistics, GIF,
r-cran-cluster 2.0.3 GNU R package for cluster analysis by Rousseeuw et al
r-cran-data.table 1.9.4 GNU R package “Extension of data.frame”
r-cran-dbi 0.3.1 GNU R package “R Database Interface”
r-cran-dichromat 2.0.0 Color schemes for dichromats
r-cran-digest 0.6.8 GNU R package “Create Cryptographic Hash Digests of R
r-cran-evaluate 0.7.2 GNU R package “Parsing and Evaluation Tools that Provide
r-cran-futile.logger 1.4.1 GNU R package “A Logging Utility for R”
r-cran-futile.options 1.0.0 GNU R package “Futile options management”
r-cran-gdata 2.17.0 GNU R package “Various R Programming Tools for Data
r-cran-gee 4.13-19 GNU R package “Generalized Estimation Equation Solver”
r-cran-getopt 1.20.0 GNU R package “C-like getopt behavior.”
r-cran-ggplot2 1.0.1 GNU R package “An Implementation of the Grammar of
r-cran-gplots 2.17.0 GNU R package “Various R Programming Tools for Plotting
r-cran-gtable 0.1.2 GNU R package “Arrange grobs in tables.”
r-cran-gtools 3.5.0 GNU R package “Various R Programming Tools”
r-cran-labeling 0.3 GNU R package “Axis Labeling”
r-cran-lambda.r 1.1.7 GNU R package “Modeling Data with Functional Programming”
r-cran-lattice 0.20-29 GNU R package “Lattice Graphics”
r-cran-leaps 2.9 GNU R package “regression subset selection”
r-cran-lme4 1.1-9 GNU R package for linear mixed effects model fitting
r-cran-locfit 1.5-9.1 Local Regression, Likelihood and Density Estimation.
r-cran-matrix 1.2-2 GNU R package of classes for dense and sparse matrices
r-cran-matrixstats 0.10.0 R package “Methods that apply to rows and columns of a matrix”
r-cran-munsell 0.4.2 GNU R package “Munsell colour system”
r-cran-nlme 3.1.122 GNU R package for (non-)linear mixed effects models
r-cran-optparse 1.2.0 GNU R package “Command line option parser.”
r-cran-permute 0.8-4 GNU R package “Functions for Generating Restricted
r-cran-plotrix 3.5-7 GNU R package “Various plotting functions”
r-cran-plyr 1.8.3 GNU R package “Tools for Splitting, Applying and Combining
r-cran-prettyr 2.0-8 GNU R package “Pretty descriptive stats.”
r-cran-propcis 0.2-5 GNU R package “PropCIs: Various confidence interval methods for proportions”
r-cran-proto 0.3-10 GNU R package “Prototype object-based programming”
r-cran-r.methodss3 1.6.1 GNU R package “Utility function for defining S3 methods”
r-cran-rapidr 0.1.1 GNU R package “RAPIDR: Reliable Accurate Prenatal non-Invasive Diagnosis.”
r-cran-rcolorbrewer 1.0-5 GNU R package providing suitable color palettes
r-cran-rcpp 0.12.1 GNU R package “Seamless R and C++ Integration”
r-cran-rcurl 1.95-4.7 GNU R package “General Network (HTTP/FTP/…) Client
r-cran-relimp 1.0-4 GNU R package “Relative Contribution of Effects in a
r-cran-reshape2 1.4.1 GNU R package “Flexibly Reshape Data: A Reboot of the
r-cran-rggobi 2.1.20 GNU R package for the GGobi data visualization system
r-cran-rgl 0.95.1247 GNU R package for three-dimensional visualisation using OpenGL
r-cran-rgtk2 2.20.31 GNU R binding for Gtk2
r-cran-rmpi 0.6-5 GNU R package interfacing MPI libraries for distributed computing
r-cran-rserve 1.7-3 GNU R Rserve tcp/ip server and sample clients
r-cran-rsqlite 1.0.0 GNU R package “SQLite Interface for R”
r-cran-rwave 2.4 GNU R package “Time-Frequency Analysis of 1-D Signals”
r-cran-samr 2.0 GNU R package “SAM: Significance Analysis of Microarrays”
r-cran-scales 0.3.0 GNU R package “Scale Functions for Visualization”
r-cran-scatterplot3d 0.3-36 GNU R package “3D Scatter Plot”
r-cran-snowfall 1.84-6 GNU R package “Easier cluster computing (based on snow).”
r-cran-sp 1:1.1-0 GNU R package “Classes and Methods for Spatial Data”
r-cran-stringr 1.0.0 GNU R package “Simple, Consistent Wrappers for Common
r-cran-tcltk2 1.2-9 GNU R package “Tcl/Tk Additions”
r-cran-testthat 0.9.1 GNU R package “Testthat code. Tools to make testing fun
r-cran-vegan 2.3-0 GNU R package “Community Ecology Package”
r-cran-waveslim 1.7.5 GNU R package “Basic wavelet routines for one-, two- and
r-cran-wavethresh 4.6.6 GNU R package “Wavelets statistics and transforms.”
r-cran-xml 3.98-1.3 GNU R package “Tools for Parsing and Generating XML Within
r-cran-xtable 1:1.7-3 GNU R coerce data to LaTeX and HTML tables
r-mathlib 3.2.2 GNU R standalone mathematics library
r-recommended 3.2.2 GNU R collection of recommended packages [metapackage]
rasmol Visualize biological macromolecules
raxml 8.0.26 Randomized Axelerated Maximum Likelihood of phylogenetic trees
ray 2.3.1 parallel de novo genome assemblies of next-gen sequencing data
ray-extra 2.3.1 Scripts and XSL sheets for post-processing for ray de novo assembler
rbs-finder 1.0 A program to find Ribosomal binding sites.
rdp-classifier 2.10.2+dfsg taxonomic assignment from next generation sequencing
readseq 1 Conversion between sequence formats
rsem 1.2.22+dfsg RNA-Seq by Expectation-Maximization
sampledata 20041011 Sample data for Bio-Linux packages
samtools 0.1.19 processing sequence alignments in SAM and BAM formats
scythe 0.993 Bayesian adapter trimmer for nextgen sequence reads
seaview 1:4.4.2 No description
seqprep 1.1 tool for stripping adaptors and/or merging paired reads with overlap
shared 1.1 Some shared files used by Bio-Linux
sickle 1.33 windowed adaptive trimming tool for FASTQ files using quality
sift 4.0.3b predicts if a substitution in a protein has a phenotypic effect
sortmerna 2.0 tool for filtering, mapping and OTU-picking NGS reads
splitstree 4.12.6 Analysis and visualisation tool for distance data from biological sequences
sputnik-mononucleotide 0.1+20101005 Searches DNA sequence files in FASTA format for microsatellite repeats
squint 1.02 Java-based multiple alignment program and editor
ssake 3.8.1 genomics application for assembling millions of very short DNA sequences
stacks 1.34 pipeline for building loci from short-read sequences
stacks-web 1.34 web interface for displaying loci from short-read sequences
staden 2.0.0b10 DNA sequence assembly (Gap4/Gap5), editing and analysis tools
staden-common 2.0.0b10 Architecture independent files for Staden
stars 1.2a STARS is an alternative interface to Staden.
sumatra 1.0.01 fast and exact comparison and clustering of sequences
swarm 1.2.20 robust and fast clustering method for amplicon-based studies
t-coffee 10.00.r1613 Multiple Sequence Alignment
tablet Graphical viewer for next gen sequence assemblies and alignments
taxinspector 1.0b3 Browser for entries in the NCBI taxonomy database
tetra 1.0b3 tetranucleotide frequency calculator with GUI
themes-v7 7.0 Graphics, icons, wallpaper and desktop settings for Bio-Linux 7
themes-v8 8.0 Graphics, icons, wallpaper and desktop settings for Bio-Linux 8
tophat 2.1.0 fast splice junction mapper for RNA-Seq reads
trace2dbest 3.14 Processes trace files into dbEST submissions
transdecoder 2.0.1+dfsg find coding regions within transcripts
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
trinityrnaseq 2.0.6+dfsg RNA-Seq De novo Assembly
trinityrnaseq-sampledata 2.0.6+dfsg RNA-Seq De novo Assembly
trnascan 1.23 tRNAscan-SE searches for tRNA genes in genomic sequences.
trnascan-se 1.3.1 search for tRNA genes in genomic sequences
tutorials 1 Tutorials and documentation for Bio-Linux users.
ugene 1.18.0+repack integrated bioinformatics toolkit
unity-lens 0.2 unity lens for Bio-Linux
usb-maker 8.2 Script to generate Bio-Linux live memory sticks.
velvet 1.2.10+dfsg Nucleic acid sequence assembler for very short reads
velvet-example 1.2.10+dfsg Example data for the Velvet sequence assembler
velvet-long 1.2.10+dfsg Nucleic acid sequence assembler for very short reads, long version
velvetoptimiser 2.2.5 Automatically optimise Velvet do novo assembly parameters
vsearch 1.1.1.nodata tool for processing metagenomic sequences
weblogo 3.3 create sequence logos from biological sequence alignments
wise 2.4.1 comparison of biopolymers, commonly DNA and protein sequences
xcut 1.4.2 A re-write of the GNU cut command with many new features.
zsh 1 Z-Shell wrapper package for Bio-Linux.