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ArchBio Linux 15.1
A Bioinformatics / Cheminformatics LiveLinux distribution


Already installed Software Packages

ArchBio LiveLinux comes with a lot of useful stuff already pre-installed, such as a TeXLive 2015 environment, Google Chromium webbrowser for access to online tools or web based data bases, several editors and development tools. This makes not only development of programs and pipelines convenient, but also usage of the tools and publication or presentation of results is made much easier. The desktop environment that comes with ArchBio Linux is Xfce4.

A list of Bioinformatics related ArchLinux packages that I maintain at the moment can be found here.

A list of pre-installed programs, libraries, and tools that are included in the ArchBio Linux distribution can be found below.

Bioinformatics Tools
Program nameVersionDescription
barriers 1.5.2 Compute local minima and energy barriers of a landscape
bedtools 2.24.0 powerful toolset for genome arithmetic
bioperl-live-git 20151119 Perl modules for bioinformatics applications.
blast+-bin 2.2.31 New suite of BLAST tools that utilizes the NCBI C++ Toolkit
clustal-omega 1.2.1 Protein sequence alignment program
clustalw 2.1 Clustal W multiple sequence alignment program, version 2.0
clustalx 2.1 Multiple alignment of nucleic acid and protein sequences
dialign 2.2.1 Multiple sequence alignment program
fragrep 2 Detect nucleotide pattern fragments in genomes that occur in a given order
gotohscan 2.0_alpha Search short sequences in large database sequences by computing all semi-global alignments
hmmer 3.1b1 Profile hidden Markov models (profile HMMs) for database searching using statistical descriptions of a sequence family's consensus
infernal 1.1.1 Search DNA sequence databases for RNA structure and sequence similarities using covariance models (CMs)
jalview 2.8.2 Bioinformatics Multiple Alignment Editor
kinwalker 2.0 Compute cotranscriptional folding trajectories of RNAs
locarna 1.8.1 Global and Local Alignment of RNAs
mafft 7.245 Multiple alignment program for amino acid or nucleotide sequences
meme 4.10.2 The MEME suite provides tools for discovering and using protein and DNA sequence motifs
muscle 3.8.31 multiple sequence comparison by log-expectation
phylip 3.696 A collection of programmes for evolutive genetics and inferring phylogenies
python-biopython 1.65 Freely available Python tools for computational molecular biology
readseq 2.1.30 A biosequence data format conversion tool
rnamicro 1.1.4 Distinguish miRNA precursor sequences from other (putative) non-coding RNAs
seaview 4.5.4 GUI for multiple sequence alignment and molecular phylogeny
snoreport 1.3 Computational identification of snoRNAs with unknown targets
tcoffee 11.00.8cbe486 An alignment tool for Protein, DNA and RNA sequences
treekin 0.3.1 Efficient computation of RNA folding dynamics
viennarna 2.1.9 RNA Secondary Structure Prediction and Comparison
Cheminformatics Tools
Program nameVersionDescription
chemtool 1.6.14 A small program for drawing chemical structures
openbabel 2.3.2 A library designed to interconvert between many file formats used in molecular modeling and computational chemistry
pymol Molecular visualization system on an Open Source foundation
Other scientific Tools
Program nameVersionDescription
gnuplot 5.0.1 Plotting package which outputs to X11, PostScript, PNG, GIF, and others
grace 5.1.25 2D plotting tool
gri 2.12.23 A script-based language for scientific graphics programming
lapack 3.5.0 Linear Algebra PACKage
blas 3.5.0 Linear Algebra PACKage
r 3.2.1 Language and environment for statistical computing and graphics
Development Tools
Program nameVersionDescription
coreutils 8.24 The basic file, shell and text manipulation utilities of the GNU operating system
ddd 3.3.12 A graphical front-end for command-line debuggers such as GDB, JDB, pydb, perl debugger...
devtools 20150606 Tools for Arch Linux package maintainers
doxygen 1.8.10
gdb 7.10 The GNU Debugger
ghex 3.10.1 A simple binary editor for the Gnome desktop
git 2.5.3 the fast distributed version control system
gitg 3.17.1 A GIT repository viewer based on GTK+
graphviz 2.38.0 Graph visualization software
swig 3.0.7 Generate scripting interfaces to C/C++ code
valgrind 3.10.1 A tool to help find memory-management problems in programs
Program nameVersionDescription
emacs 24.5 The extensible, customizable, self-documenting real-time display editor
gedit 3.16.3 A text editor for GNOME
meld 3.14.0 Visual diff and merge tool
nedit 5.6a A Unix text editor for programmers and general users
vim 7.4.854
xournal 0.4.8 Notetaking and sketching application
Graphics Tools
Program nameVersionDescription
gimp 2.8.14 GNU Image Manipulation Program
inkscape 0.91 Vector graphics editor using the SVG file format
xfig 3.2.5c An interactive drawing tool

Download / Install

Get the latest ArchBio Live Linux: ArchBio-v15.1-x86_64.iso (architecture: x86 64bit, size: 1.9GB)

Prepare an USB-stick

Insert your USB-stick and make sure that it is not mounted. Replace the X with the corresponding device character of your USB-stick and execute the below command as root:

# dd bs=4M if=/path/to/iso/file of=/dev/sdX && sync
Alternatively, if you are using Windows, or MacOS X, you find out about more options how to prepare an USB stick for the use of ArchBio in the corresponding ArchLinux Wiki Page "USB flash installation media".