Molecular Linux
Molecular Biology related programs for Linux

(sorted by categories)

AbacusABaCUS is a no-frills program developed to investigate the significance of the putative correspondence between exons and units of protein structure.
AcedbAcedb is a genome database system originally developed for the C.elegans genome project
AMMPa modern full-featured molecular mechanics, dynamics and modeling program.
AmpliconProgram for designing group-specific PCR primer sets
AnglerA Browser of C.elegans Embryo Development In Time and Space
ARBMicrobiologist's sequence database tool
Arkagraphical interface for the programs from the GP (Genpak) package
Artemisa DNA sequence viewer and annotation tool that allows visualization of sequence features and the results of analyses within the context of the sequence, and its six-frame translation.
ATVa phylogenetic tree display tool
autoseqa small package of base calling software for ABI automated DNA sequencers
Babela program designed to interconvert a number of file formats currently used in molecular modeling
BiogrepA grep that is optimized for biosequences. Biogrep is designed to locate large sets of patterns in sequence databases in parallel.
BioJavaThe BioJava Project is an open-source project dedicated to providing Java tools for processing biological data. is a public resource supporting scientists who use Lisp to develop intelligent applications in the biological sciences.
BioMailautomate searching for recent scientific papers in the PubMed Medline database
Bioperl open source Perl tools for bioinformatics, genomics and life science research
BiopythonThe Biopython Project is an international association of developers of freely available Python tools for computational molecular biology.
BioWishBiowish is a C-extension for the Tcl/Tk scripting language
BlastBLAST (Basic Local Alignment Search Tool) is a set of similarity search programs designed to explore all of the available sequence databases
BlixemBlixem, which stands for "BLast matches In an X-windows Embedded Multiple alignment", is an interactive browser of pairwise Blast matches that have been stacked up in a "master-slave" multiple alignment.
BRAGIBRAGI is a interactive protein modelling and display program. It was developed for the special purpose to modell unknown proteins from the structure of a known one
caRNAcRNA secondary structure inference for set of homologous sequences
caRNAstaComparative Analysis of RNA structures by Tree Alignment
ChimeraExcellent molecular graphics package with support for a wide range of operations, i ncluding flexible molecular graphics, high resolution images for publication, user-driven analysis, multiple sequence alignment analysis, multiple model analysis, dockin
ClannClann: Software for investigating phylogenomic information using supertrees. This implements several methods of Supertree analysis (which are used as optimality criteria) and allows exhaustive and heuristic searches of tree-space to find the best supert
clustalwThe famous ClustalW multiple alignment program
clustalxClustal X provides a window-based user interface to the ClustalW multiple alignment program
CNS The 'Crystallography & NMR System' for macromolecular structure anaylsis
consedA Unix-based Graphical Editor and Automated Finishing Program for Phrap Sequence Assemblies
ConsInspectorA tool for the prediction of protein binding sites in nucleic acids
coveCOVE is an implementation of stochastic context free grammar methods for RNA sequence/structure analysis.
DBWatcherDBWatcher is a program handling periodic BLAST searches to find similarities to your own sequences.
DCSEDCSE (Dedicated Comparative Sequence Editor) is a multiple alignment editor
Deep View Swiss-PdbViewerSwiss-PdbViewer is an application that provides a user friendly interface allowing to analyse several proteins at the same time
DIALIGNDIALIGN is an alignment program that relies on comparison of whole segments of the sequences instead of comparison of single residue
DINOa realtime 3D visualization program for structural biology data.
DNA-GUIDNA Graphical User Interface
DomainFinderDomainFinder 1.0 DomainFinder is an interactive program for the determination and characterization of dynamical domains in proteins
EMBOSSEMBOSS is a package of high-quality FREE Open Source software for sequence analysis.
Ensemblsoftware system which produces and maintains automatic annotation on eukaryoticgenomes
fastDNAmlEstimates maximum likelihood phylogenetic trees from nucleotide sequences
FriendFriend, an Integrated Front-end Application for Bioinformatics
Garlica free molecular visualization program
gBioSeqBiological sequence (ADN, protein) editor for GTK/Linux
GDE The GDE is a set of programs for multiple sequence alignment and analysis.
GDISa GTK based program for the display and manipulation of isolated molecules and periodic systems
GEANFAMMERGEnome ANalysis and Protein FAMily MakER
geneid Gene prediction tool, it can also introduce homology and annotation evidences and produce a reannotation of a genomic sequence. A pthreads parallel version also available.
GeneView IIInteractive GenBank Entry Visualization
GenomeInspectorSoftware for the analysis of spatial correlations of elements on DNA sequences
GenomePixelizerGenome Visualization Tool: Detection of duplicating events in genomes, Displaying the Genetic Maps, Comparative genetics in general.
Genpaka set of small utilities written in ANSI C to manipulate DNA sequences in a Unix fashion, fit for combining within shell and cgi scripts
gff2psConverting genomic annotations in GFF format to PostScript
GRILGRIL automates the process of identifying large-scale genome inversions and rearrangements
GromacsThe World' s fastest Molecular Dynamics - and it' s gpl
GRSA Graphic Tool for Genome Retrieval and Segment Analysis
HMMERProfile hidden Markov models for biological sequence analysis
io_libAn open source C library of sequence trace files supporting ABI, ALF, SCF, CTF and ZTR file formats.
JAlignerJAligner is a Java implementation of biological sequence alignment algorithms.
JalviewJalview - a java multiple alignment editor
Kintecus Run chemical kinetics/fitting of catalyst reactor, and enzyme reactions
Leksbotan explanatory dictionary of botanic and biological terms
LIBELLULALIBELLULA is a neural network based web server to evaluate fold recognition results
libGenomeA cross platform C++ development library to manipulate DNA and protein sequences. It can read and write sequence and annotation data in several file formats.
MAExplorerThe Microarray Explorer (MAExplorer) is a Java-based data-mining facility for microarray databases run as a stand-alone program. It includes graphics, statistics, clustering, reports, data filtering.
MauveMauve is a multiple genome alignment and visualization package that considers large-scale rearrangements in addition to nucleotide substitution and indels.
MELTINGAccurate computation of the enthalpy, entropie and melting temperature of a nucleic acid duplex
MeltSimCalculation of DNA melting curves and maps using the Poland-Scheraga algorithm and empirical constraints by R.D. Blake.
MMTK-2.2molecular modeling tool-kit 2.2
MODELLERa program for homology protein structure modelling by satisfaction of spatial restraints.
ModViewModView is a program to visualize and analyze multiple biomolecule structures and/or sequence alignments.
MOLPHYA Computer Program Package for Molecular Phylogenetics including ProtML
MOPAC7a general-purpose semi-empirical molecular orbital package for the study of chemical structures and reactions.
mpiBLASTmpiBLAST is a parallel implementation of NCBI-BLAST that uses database segmentation. It achieves a super-linear speedup in some cases.
MPSRCH MPSRCH (tm) is a suite of Smith-Waterman sequence analysis programs which run under Linux and Tru64 on Intel and Alpha.
MSPcruncha BLAST enhancement filter
MuscaMultiple sequence alignment of aa or nucleotide sequences / uses pattern discovery
MUSCLEMultiple sequence alignment. More accurate than T-Coffee, faster than CLUSTALW.
NAMD NAMD is a parallel, object-oriented molecular dynamics code designed for high-performance simulation of large biomolecular systems.
NCRNASCANa structural RNA genefinder
njplotNJplot is a tree drawing program able to draw any binary tree expressed in the standard phylogenetic tree format
OmniGeneStandardizing Biological Data Interchange Through Web Services Technology
On-line Genome AnnotationsAnnotations for many eukaryotic, bacterial and archaeal genomes. Can be searched using accession numbers or sought features
OsletA molecular modeling and simulation environment in Java, mainly for education.
PAMLPhylogenetic Analysis by Maximum Likelihood
PatScanPatScan is a pattern matcher which searches protein or nucleotide (DNA, RNA, tRNA etc.) sequence archives for instances of a pattern which you input
PaupSoftware package for inference of evolutionary trees
PHASEPHASE performs molecular phylogenetic inference using maximum likelihood and Bayesian (MCMC) techniques. Specific RNA substitution models are implemented to account for the correlated mutations of paired bases in RNA helices.
phrapa program for assembling shotgun DNA sequence data
phredPhred reads DNA sequencer trace data, calls bases, assigns quality values to the bases, and writes the base calls and quality values to output files.
PHYLIPPHYLIP is a free package of programs for inferring phylogenies.
PhyloDraw PhyloDraw is a drawing tool for creating phylogenetic trees. PhyloDraw supports various kinds of multialignment programs (Dialign2, Clustal-W, Phylip format, and pairwise distance matrix) and visualizes various kinds of tree diagrams, e.g. rectangular cl
PhyloGrapherPhyloGrapher is a program designed to visualize and study evolutional relationship between families of homologous genes or proteins. PhyloGrapher is a drawing tool that generates custom graphs out of the given set of genes based on distance matrix file.
phylowinPhylo_win is a graphical colour interface for molecular phylogenetic inference.
PKNOTSRNA pseudoknot prediction
PopulationsPopulation genetic software (individuals or populations distances, phylogenetic trees)
Pratta pattern discovery tool
primera program for picking primers for PCR reaction
ProSAProSA is a useful web application for finding known protein domains in nucleotide/protein sequences via PROSITE database searching
PyMolPyMOL is a molecular graphics system with an embedded Python interpreter designed for real-time visualization and rapid generation of high-quality molecular graphics images and animations.
PyPhyPyPhy is a set of python scripts and modules for automatic, large-scale reconstructions of phylogenetic relationships of complete microbial genomes.
rasmolRasMol is a free program which displays molecular structure.
readseqReads and writes nucleic/protein sequences in various format
RNA GENiEA web based program for the prediction of rna genes in genomic DNA sequences
RNABOBRNABOB -- fast RNA motif/pattern searcher
RnaViza user-friendly, portable, GUI program for producing publication-quality secondary structure drawings of RNA molecules. Drawings
SAM equence Alignment and Modeling Systea collection of flexible software tools for creating, refining, and using linear hidden Markov models for biological sequence analysis
SEALSSEALS (A System for Easy Analysis of Lots of Sequences) is a software package expressly designed for large-scale research projects in bioinformatics.
seaviewSeaView is a graphical multiple sequence alignment editor
SEPONSEPON designs gene-specific oligonucleotides for microarray experiments and is able to use EST input from organisms in which the genome is not annotated for genes. SEPON implements a novel algorithm for reducing cross-hybridization by utilizing thermodyna
SeqPupSeqPup biological sequence editor and analysis program
ShadyBox.ShadyBox. The FIRST GUI based WYSIWYG multiple sequence alignment drawing program for Major Unix platforms
SightAllows programming free assembling of web resoureces, local executables and ssh services into arbitrary workflow.
sp2fastaproduce a file in FASTA format from one in SWISSPROTor EMBL flat file format
Spocka full-featured molecular graphics program
Staden PackageThis is a free to academics (charge for commercial users) package including sequence assemble, trace viewing/editing and sequence analysis tools. It also includes a GUI to the free EMBOSS suite.
StericA Program to Calculate the Steric Size of Molecules about a Point in terms of their Cone Angles and Solid Angles, as well as their total Volumes and Projected Areas
Teiresias-based Association DiscoveryDiscover associations in your data set (gene expression analysis, phenotype analysis, etc.)
Teiresias-based Gene expression analysisDiscover patterns in microarray data using the Teiresias algorithm. Allows discovery of inversely regulated genes.
ToucanA Java tool for regulatory sequence analysis: detecting over-represented motifs and modules in sets of co-regulated genes.
TREE-PUZZLE:TREE-PUZZLE: Maximum likelihood analysis for nucleotide, amino acid, and two-state data
tRNAscan-SEtRNA detection in genome sequences, detects ~99% of eukaryotic nuclear or prokaryotic tRNA genes, with a false positive rate of less than one per 15 gigabases, and with a search speed of about 30 kb/second.
UltraScanUltraScan is a comprehensive GUI editing and data analysis package for hydrodynamic data from analytical ultracentrifugation experiments
unrootedUnrooted is a tree drawing program able to draw any binary tree expressed in the standard phylogenetic tree format in an unrooted way, that is, using a circular shape, with labels aligned with terminal branches.
VEGA VEGA was developed to create a bridge between most of the molecular software packages, like BioDock, Quanta/CHARMm, Insight II, MoPac, etc. In this tool have been also implemented some features that are useful to analyze, display and manage the 3D struct
VEILA hidden Markov model for finding genes in vertebrate DNA 
Vienna RNA PackageRNA Secondary Structure Prediction and Comparison
VMDVMD is a molecular visualization program for displaying, animating, and analyzing large biomolecular systems using 3-D graphics and built-in scripting
WHAT IFWHAT IF is a versatile protein structure analysis program that can be used for mutant prediction, structure verification, molecular graphics, etc
WU-BlastWashington U. Blast
XMolCalca small utility that allows you to calculate a molecular weight
xsactEST clustering tool
ZDOCKProtein-protein complex structure prediction software
158 entries

Files ending with .tgz or .tar.gz, are tar'ed and gnuzipped files, unpack them with: tar xvzf myfile.tgz
Files ending with .gz are gnuzipped , unpack them with : gunzip myfile.gz
(Some browsers like Netscape don't recognize gzipped files ... if you get garbage on your screen, try to hold down the SHIFT key (Alt on a Mac) while clicking on the file.)

A program missing ?? Comments ?? Links outdated ??

Please mail me or log in to use the online form.
Key Resource
Linux Software

Sicheritz-Ponten Thomas, Ph.D,         (
Center for Biological Sequence Analysis                   \
BioCentrum-DTU, Technical University of Denmark            )
CBS: +45 45 252485      Building 208, DK-2800 Lyngby  ##----->
Fax: +45 45 931585       )
     ... damn arrow eating trees ...                     (