The Linux for Biotechnology project (LfB) is dedicated to compiling the most
comprehensive collection of Biotechnology software, and making it
available for the Linux operating system. LfB provides
point-and-click installation, a complete on-line library of searchable
documentation, and much more.
The packages on LfB represent the
state-of-the-art in Biotechnology data processing, and are
identical to the versions used on high end scientific
The combination of ever decreasing hardware prices, and the superb
Linux operating system, now makes it possible to use these same
packages on a "standard" personal computer.
The current LfB distribution contains Linux versions of the following
Biotechnology data reduction and analysis packages :
- abacus - Analysis of Blake's Conjecture Using Simulations
- ae2 - Sequence alignment editor
- alfresco - Comparitive sequence analysis
- artemis - DNA sequence viewer and annotation tool
- beta - Estimation of alpha - Nonparametric linkage analysis
- biomail - web-based application for medical researchers and biologists.
- bioperl - perl tools for Molecular biology
- biopython - Python tools for Molecular biology
- codonW- A package for codon usage analysis.
- DEODAS - DEgenerate Oligonucleotide Design & Analysis System
- Distutils - Python distribution tools
- DND - Protein molecular dynamics simulation/visualization
- DomainFinder - An interactive program for the determination and characterization of dynamical domains in proteins.
- dx - Data Explorer, visualisation package
- e-PCR - Sequence mapping by Electronic PRC
- EdIt - An automatic editor for DNA sequence data
- efetch - Retrieve entries from sequence databases
- EMBOSS - EMB Open Source Software
- ESPript - Creates postrcipt sequence renderings
- fastlink - Genetic linkage computations
- garlic - Molecular visualization
- GenoCheck - A method for detecting errors in pedigree data
- genpak - Utilities to manipulate DNA sequences
- gmaes - Evolution simulations
- gperiodic - Periodic table
- gibbs - Calculation of Probabilities for Diallelic Traits on Complex Pedigrees
- hmmer - Biological sequence analysis using profile hidden Markov models
- ImageJ - Java Image viewer
- jalview - a java multiple alignment editor
- jmol - an open-source molecule viewer and editor
- kmol - Molecular weight calculator
- ldb_2b - Hybrid mapping
- LEKSBOT - a botanical lexicon
- lintre - Phylogenetic tests of the molecular clock and linearized tree
- melting - nearest-neighbor computation of nucleic acid hybridation
- MIRA - DNA shotgun sequence data assembler
- mmlib - A C++ macromolecular class library
- mmtool - A macromolecular visualisation tool
- pdbtool - A macromolecular visualisation tool
- moldy - a general-purpose molecular dynamics simulation program
- ncbi-tools - NCBI Software Development Toolkit was developed for the production and distribution of GenBank, Entrez, BLAST, and related services by NCBI.
- Blastall - NHGRI Blastall (a perl interface)
- njbafd - Neighbor-joining tree construction from allele frequency data
- njbtie - search all tie neighbor-joining trees and UPGMA trees and for bootstrapping
- oligomap - OLIGOMAP is a tool to help researchers engineer restriction sites into oligonucleotides by silent mutagenesis
- orfind - orfind is a command line version of ORF Finder (http://www.ncbi.nlm.nih.gov/gorf/gorf.html)
- pdb2cif - convert PDB to CIF format
- pftools - pftools is a collection of experimental programs supporting the generalized profile format and search method of PROSITE and NUCSITE.
- pima - Pattern-Induced Multi-sequence Alignment program
- pseudoknots - An extension of the Zuker M FOLD algorithm to optimal minimum energy prediction of pseudoknotted RNA structures
- plato - Partial likelihoods expressed through optimisation
- primer3 - Primer3 picks primers for PCR reactions
- PSPP - Statistical analysis package.
- puzzle - Maximum likelihood analysis for nucleotide, amino acid, and two-state data
- PSeq-Gen - An application for the Monte Carlo simulation of protein sequence evolution along phylogenetic trees
- QDate - Estimates date of divergence using data for sequence parirs
- QuickPDB - Java Applet to view Protein Data Bank
- rhmapper - A package for creating radiation hybrid maps
- rnabob - searches for RNA motifs in sequence databases
- SampLin - Data Acquisition package
- sc_rate - Evaluates the quality of any sequence alignment.
- Topal - Package for Detecting Recombination Breakpoints
- RasMol2 - molecular graphics program intended for the visualisation of proteins, nucleic acids and small molecules.
- pasu - Probability and Statistics Utilities
- PVM - Parallel Virtual Machine
- PyMOL - molecular graphics program designed for rapid and efficient generation of high-quality molecular graphics animations.
- seals - System for Easy Analysis of Lots of Sequences
- sendbs - Average nucleotide diversity within and between populations
- sequin - Program to aid submission of sequences to GenBank, EMBL and DDJB
- seqsplit - Programs for running blastx on very long queries
- sibs - Sib Pair Analysis
- simPCR - check an sfind file from GCG for sequences that have homology to 2 opposite primers.
- sog - algorithm to find the most parsimoneous nucleotide phylogenetic tree
- TipDate - A program to estimate the rate of molecular evolution and time-scale of a phylogeny from dated sequences.
- tRNAscan - a program for improved detection of transfer RNA genes in genomic sequence
- treevolve - a program to simulate the evolution of DNA sequences under different population dynamic scenarios
- vanilla - command line programs (written in Java) to provide simple access to the functionality of PAL
- vaspview - scientific visualization package for
examining output files generated by the Vienna Ab-initio Simulation Package
- w2h - WWW interface to the GCG Sequence Analysis Software Package
- wise - DNA and protein sequence comparison package
LfB also now includes a set of graphical and database tools, tools for
enhancing the security of your Linux system, and a remote desktop
All the applications have been tested with the
Linux system distributions from
RedHat (version 6.2) and
SuSE (version 6.4).
(a full listing of contents of the current release is available
here, please note that this is
a large file download.)
The collection has been assembled with the assistance
of the worldwide Biotechnology software community.
The system includes an integrated set of documentation
in HTML format, and many packages include PostScript
format documents. Source code is included where permitted by
the package license holders.