Molecular Linux
Molecular Biology related programs for Linux

sorted by keywords ... (kind of)

3D structure visualization ABI ABI DNA Sequencer affine gap alignment alignment editor alignment program alignment viewer amplification analysis analytical ultracentrifugation Aneda assembly automated phylogenetic analysis base calling Bayesian Bayesian methods BioCoRE bioinformatics biological macromolecule biological sequence editor biosequence blast blast filter bond and atom rendering C.elegans cafasp casp chemical kinetics enzyme kinetics combustion catalyst reactor CSTR modeling software chemical structures chromatogram code generators comparative analysis Comparative genetics composition correlation crystallography data analysis data flow data mining database database interface database searching database segmentation denaturation dictionary distance correlations DNA melting DNA sequence viewer DNA sequencing DNA structure drawing Duplications duplications. electron density maps embl emboss EST EST clustering similarity alignment eva evolution Evolution. exons extension file conversion surface mapping finite element fold recognition format converter friend GenBank Entry Visualization gene duplications gene expression gene expression analysis gene finding gene regulation gene-expression gene-finding gene-prediction genetic distances genome annotation genome annotations genome development library C++ sequence manipulation GenBank DNAstar FastA genome rearrangement inversion locator large-scale recombination Genome Retrieval Genomes genomic annotation genomic database system genomics GFF global fitting gotoh's improvement Graph theory grep group-specific Hidden Markov Models HMM homologous genes inference java library maximum likelihood Maximum likelihood analysis Maximum Likelihood Inference of Protein Phylogeny maximum likelihood phylogenetic trees MCMC medline melting temperature microarray microarray analysis microarray analysis software modeling Molecular Dynamics high performance simulator molecular dynamics modeling pdb force field molecular dynamics simulations molecular editor molecular graphics molecular mechanics molecular modeling molecular modelling molecular rendering molecular simulations molecular structure analysis molecular visualization molecular visualization program molecular weight monte carlo motif MPI multiple multiple alignment editor multiple genome alignment comparison rearrangement multiple protein structure visualization multiple sequence alignment multiple sequence alignment analys is multiple sequence alignment drawing program mysql NAMD neural networks neural net nmr nucleic acid oligonucleotide online searching online tools parallel pattern pattern discovery pattern matcher pattern matching PCR PDB perl Phase phenotype analysis phylogenetic phylogenetic tree Phylogenetic tree reconstruction phylogenetic trees phylogenomics Phylogenomics phylogeny tree supertree genomic Phylogeny PostScript POV-Ray scenes prediction primer primer selection program PROSITE protein binding sites protein docking protein domains protein families protein interaction protein modelling protein structure protein structure modelling protein structure prediction protein/DNA/RNA family clustering pubmed python real-time visualization reannotation regex regular expression regulatory sequence analysis rendered animations RNA RNA folding RNA gene finder RNA motif RNA pseudoknots RNA secondary structure RNA secondary structures SCF secondary structure SEPON sequence Sequence Alignment sequence analysis sequence comparisons sequence conversion sequence database sequence editor sequence finishing sequence patterns sequence similarity sequence utiities sequences sequencing Smith-Waterman Solid Angle calculation staden statistic mechanics Steric Size calculation structural alignments structural biology structure structure analysis structure prediction stuctures substitution substitution rates swissprot Tcl/Tk thermodynamics threading trace trace chromatogram trace files trajectory analysis transcription factor binding sites transcription factors tree tree of life tree viewer tRNA searching visualisation visualization VMD Web robots workflow xchange biological data

3D structure visualization

PyMol

PyMOL 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.

ABI

autoseq	a small package of base calling software for ABI automated DNA sequencers
phrap	a program for assembling shotgun DNA sequence data
phred	Phred reads DNA sequencer trace data, calls bases, assigns quality values to the bases, and writes the base calls and quality values to output files.
Staden Package	This 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.

ABI DNA Sequencer

autoseq

a small package of base calling software for ABI automated DNA sequencers

affine gap

JAligner

JAligner is a Java implementation of biological sequence alignment algorithms.

alignment

Blixem	Blixem, 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.
Chimera	Excellent 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
clustalw	The famous ClustalW multiple alignment program
clustalx	Clustal X provides a window-based user interface to the ClustalW multiple alignment program
DCSE	DCSE (Dedicated Comparative Sequence Editor) is a multiple alignment editor
Deep View Swiss-PdbViewer	Swiss-PdbViewer is an application that provides a user friendly interface allowing to analyse several proteins at the same time
DIALIGN	DIALIGN is an alignment program that relies on comparison of whole segments of the sequences instead of comparison of single residue
gBioSeq	Biological sequence (ADN, protein) editor for GTK/Linux
JAligner	JAligner is a Java implementation of biological sequence alignment algorithms.
Jalview	Jalview - a java multiple alignment editor
Mauve	Mauve is a multiple genome alignment and visualization package that considers large-scale rearrangements in addition to nucleotide substitution and indels.
ModView	ModView is a program to visualize and analyze multiple biomolecule structures and/or sequence alignments.
Musca	Multiple sequence alignment of aa or nucleotide sequences / uses pattern discovery
MUSCLE	Multiple sequence alignment. More accurate than T-Coffee, faster than CLUSTALW.
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
SAM equence Alignment and Modeling Syste	a collection of flexible software tools for creating, refining, and using linear hidden Markov models for biological sequence analysis
seaview	SeaView is a graphical multiple sequence alignment editor
ShadyBox.	ShadyBox. The FIRST GUI based WYSIWYG multiple sequence alignment drawing program for Major Unix platforms
xsact	EST clustering tool

alignment editor

DCSE	DCSE (Dedicated Comparative Sequence Editor) is a multiple alignment editor
gBioSeq	Biological sequence (ADN, protein) editor for GTK/Linux
Jalview	Jalview - a java multiple alignment editor
ModView	ModView is a program to visualize and analyze multiple biomolecule structures and/or sequence alignments.
seaview	SeaView is a graphical multiple sequence alignment editor

analysis

ARB	Microbiologist's sequence database tool
BioJava	The BioJava Project is an open-source project dedicated to providing Java tools for processing biological data.
Biopython	The Biopython Project is an international association of developers of freely available Python tools for computational molecular biology.
BioWish	Biowish is a C-extension for the Tcl/Tk scripting language
Blast	BLAST (Basic Local Alignment Search Tool) is a set of similarity search programs designed to explore all of the available sequence databases
caRNAc	RNA secondary structure inference for set of homologous sequences
Chimera	Excellent 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
clustalw	The famous ClustalW multiple alignment program
clustalx	Clustal X provides a window-based user interface to the ClustalW multiple alignment program
CNS	The 'Crystallography & NMR System' for macromolecular structure anaylsis
DNA-GUI	DNA Graphical User Interface
EMBOSS	EMBOSS is a package of high-quality FREE Open Source software for sequence analysis.
Friend	Friend, an Integrated Front-end Application for Bioinformatics
MAExplorer	The 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.
MPSRCH	MPSRCH (tm) is a suite of Smith-Waterman sequence analysis programs which run under Linux and Tru64 on Intel and Alpha.
NCRNASCAN	a structural RNA genefinder
PatScan	PatScan is a pattern matcher which searches protein or nucleotide (DNA, RNA, tRNA etc.) sequence archives for instances of a pattern which you input
PKNOTS	RNA pseudoknot prediction
Pratt	a pattern discovery tool
PyPhy	PyPhy is a set of python scripts and modules for automatic, large-scale reconstructions of phylogenetic relationships of complete microbial genomes.
readseq	Reads and writes nucleic/protein sequences in various format
SEALS	SEALS (A System for Easy Analysis of Lots of Sequences) is a software package expressly designed for large-scale research projects in bioinformatics.
sp2fasta	produce a file in FASTA format from one in SWISSPROTor EMBL flat file format
Staden Package	This 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.
Teiresias-based Association Discovery	Discover associations in your data set (gene expression analysis, phenotype analysis, etc.)
Teiresias-based Gene expression analysis	Discover patterns in microarray data using the Teiresias algorithm. Allows discovery of inversely regulated genes.
Toucan	A 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-SE	tRNA 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.
UltraScan	UltraScan is a comprehensive GUI editing and data analysis package for hydrodynamic data from analytical ultracentrifugation experiments
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
WU-Blast	Washington U. Blast

analytical ultracentrifugation

UltraScan

UltraScan is a comprehensive GUI editing and data analysis package for hydrodynamic data from analytical ultracentrifugation experiments

Aneda

MPSRCH

MPSRCH (tm) is a suite of Smith-Waterman sequence analysis programs which run under Linux and Tru64 on Intel and Alpha.

assembly

consed	A Unix-based Graphical Editor and Automated Finishing Program for Phrap Sequence Assemblies
phrap	a program for assembling shotgun DNA sequence data
Staden Package	This 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.

automated phylogenetic analysis

PyPhy

PyPhy is a set of python scripts and modules for automatic, large-scale reconstructions of phylogenetic relationships of complete microbial genomes.

base calling

autoseq	a small package of base calling software for ABI automated DNA sequencers
phred	Phred reads DNA sequencer trace data, calls bases, assigns quality values to the bases, and writes the base calls and quality values to output files.

Bayesian

PAML	Phylogenetic Analysis by Maximum Likelihood
PHASE	PHASE 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.

Bayesian methods

PAML	Phylogenetic Analysis by Maximum Likelihood

BioCoRE

NAMD	NAMD is a parallel, object-oriented molecular dynamics code designed for high-performance simulation of large biomolecular systems.

bioinformatics

Friend

Friend, an Integrated Front-end Application for Bioinformatics

biological macromolecule

Garlic

a free molecular visualization program

biological sequence editor

SeqPup

SeqPup biological sequence editor and analysis program

biosequence

Biogrep

A grep that is optimized for biosequences. Biogrep is designed to locate large sets of patterns in sequence databases in parallel.

blast

Blixem	Blixem, 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.
DBWatcher	DBWatcher is a program handling periodic BLAST searches to find similarities to your own sequences.
mpiBLAST	mpiBLAST is a parallel implementation of NCBI-BLAST that uses database segmentation. It achieves a super-linear speedup in some cases.
MSPcrunch	a BLAST enhancement filter
WU-Blast	Washington U. Blast

blast filter

Blixem	Blixem, 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.
MSPcrunch	a BLAST enhancement filter

bond and atom rendering

Spock

a full-featured molecular graphics program

C.elegans

Angler

A Browser of C.elegans Embryo Development In Time and Space

cafasp

LIBELLULA

LIBELLULA is a neural network based web server to evaluate fold recognition results

casp

LIBELLULA

LIBELLULA is a neural network based web server to evaluate fold recognition results

chemical kinetics enzyme kinetics combustion catalyst reactor CSTR modeling software

Kintecus

Run chemical kinetics/fitting of catalyst reactor, and enzyme reactions

chemical structures

MOPAC7

a general-purpose semi-empirical molecular orbital package for the study of chemical structures and reactions.

chromatogram

io_lib	An open source C library of sequence trace files supporting ABI, ALF, SCF, CTF and ZTR file formats.
phrap	a program for assembling shotgun DNA sequence data
phred	Phred reads DNA sequencer trace data, calls bases, assigns quality values to the bases, and writes the base calls and quality values to output files.

code generators

Sight

Allows programming free assembling of web resoureces, local executables and ssh services into arbitrary workflow.

comparative analysis

caRNAc

RNA secondary structure inference for set of homologous sequences

Comparative genetics

GenomePixelizer

Genome Visualization Tool: Detection of duplicating events in genomes, Displaying the Genetic Maps, Comparative genetics in general.

composition

RNA GENiE

A web based program for the prediction of rna genes in genomic DNA sequences

correlation

GenomeInspector	Software for the analysis of spatial correlations of elements on DNA sequences
PHASE	PHASE 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.

crystallography

CNS	The 'Crystallography & NMR System' for macromolecular structure anaylsis

data analysis

UltraScan

UltraScan is a comprehensive GUI editing and data analysis package for hydrodynamic data from analytical ultracentrifugation experiments

data flow

Sight

Allows programming free assembling of web resoureces, local executables and ssh services into arbitrary workflow.

data mining

Teiresias-based Association Discovery	Discover associations in your data set (gene expression analysis, phenotype analysis, etc.)
Teiresias-based Gene expression analysis	Discover patterns in microarray data using the Teiresias algorithm. Allows discovery of inversely regulated genes.

database

Acedb	Acedb is a genome database system originally developed for the C.elegans genome project
ARB	Microbiologist's sequence database tool
Friend	Friend, an Integrated Front-end Application for Bioinformatics
HMMER	Profile hidden Markov models for biological sequence analysis
ModView	ModView is a program to visualize and analyze multiple biomolecule structures and/or sequence alignments.
mpiBLAST	mpiBLAST is a parallel implementation of NCBI-BLAST that uses database segmentation. It achieves a super-linear speedup in some cases.

database interface

ModView

ModView is a program to visualize and analyze multiple biomolecule structures and/or sequence alignments.

database searching

HMMER

Profile hidden Markov models for biological sequence analysis

database segmentation

mpiBLAST

mpiBLAST is a parallel implementation of NCBI-BLAST that uses database segmentation. It achieves a super-linear speedup in some cases.

denaturation

MeltSim

Calculation of DNA melting curves and maps using the Poland-Scheraga algorithm and empirical constraints by R.D. Blake.

dictionary

Leksbot

an explanatory dictionary of botanic and biological terms

distance correlations

GenomeInspector

Software for the analysis of spatial correlations of elements on DNA sequences

DNA melting

MeltSim

Calculation of DNA melting curves and maps using the Poland-Scheraga algorithm and empirical constraints by R.D. Blake.

DNA sequence viewer

Artemis

a 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.

DNA sequencing

consed	A Unix-based Graphical Editor and Automated Finishing Program for Phrap Sequence Assemblies
phrap	a program for assembling shotgun DNA sequence data
phred	Phred reads DNA sequencer trace data, calls bases, assigns quality values to the bases, and writes the base calls and quality values to output files.

DNA structure

Garlic

a free molecular visualization program

drawing

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
ShadyBox.	ShadyBox. The FIRST GUI based WYSIWYG multiple sequence alignment drawing program for Major Unix platforms

Duplications

GEANFAMMER	GEnome ANalysis and Protein FAMily MakER
GenomePixelizer	Genome Visualization Tool: Detection of duplicating events in genomes, Displaying the Genetic Maps, Comparative genetics in general.
PhyloGrapher	PhyloGrapher 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.

duplications.

PhyloGrapher

PhyloGrapher 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.

electron density maps

Deep View Swiss-PdbViewer

Swiss-PdbViewer is an application that provides a user friendly interface allowing to analyse several proteins at the same time

embl

consed	A Unix-based Graphical Editor and Automated Finishing Program for Phrap Sequence Assemblies
phrap	a program for assembling shotgun DNA sequence data
sp2fasta	produce a file in FASTA format from one in SWISSPROTor EMBL flat file format
Staden Package	This 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.

emboss

Staden Package

This 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.

EST

SEPON	SEPON 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
xsact	EST clustering tool

EST clustering similarity alignment

xsact

EST clustering tool

eva

GRS	A Graphic Tool for Genome Retrieval and Segment Analysis
LIBELLULA	LIBELLULA is a neural network based web server to evaluate fold recognition results

evolution

GenomePixelizer	Genome Visualization Tool: Detection of duplicating events in genomes, Displaying the Genetic Maps, Comparative genetics in general.
PHASE	PHASE 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.

Evolution.

GenomePixelizer

Genome Visualization Tool: Detection of duplicating events in genomes, Displaying the Genetic Maps, Comparative genetics in general.

exons

Abacus

ABaCUS is a no-frills program developed to investigate the significance of the putative correspondence between exons and units of protein structure.

extension

BioWish

Biowish is a C-extension for the Tcl/Tk scripting language

file conversion surface mapping

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

finite element

UltraScan

UltraScan is a comprehensive GUI editing and data analysis package for hydrodynamic data from analytical ultracentrifugation experiments

fold recognition

LIBELLULA

LIBELLULA is a neural network based web server to evaluate fold recognition results

format converter

Babel

a program designed to interconvert a number of file formats currently used in molecular modeling

friend

Friend

Friend, an Integrated Front-end Application for Bioinformatics

GenBank Entry Visualization

GeneView II

Interactive GenBank Entry Visualization

gene duplications

GEANFAMMER

GEnome ANalysis and Protein FAMily MakER

gene expression

MAExplorer	The 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.
Teiresias-based Association Discovery	Discover associations in your data set (gene expression analysis, phenotype analysis, etc.)

gene expression analysis

Teiresias-based Association Discovery

Discover associations in your data set (gene expression analysis, phenotype analysis, etc.)

gene finding

VEIL	A hidden Markov model for finding genes in vertebrate DNA�

gene regulation

Toucan

A Java tool for regulatory sequence analysis: detecting over-represented motifs and modules in sets of co-regulated genes.

gene-expression

SEPON

SEPON 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

gene-finding

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.

gene-prediction

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.

genetic distances

Populations

Population genetic software (individuals or populations distances, phylogenetic trees)

genome annotation

Artemis	a 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.
Ensembl	software system which produces and maintains automatic annotation on eukaryoticgenomes
On-line Genome Annotations	Annotations for many eukaryotic, bacterial and archaeal genomes. Can be searched using accession numbers or sought features

genome annotations

On-line Genome Annotations

Annotations for many eukaryotic, bacterial and archaeal genomes. Can be searched using accession numbers or sought features

genome development library C++ sequence manipulation GenBank DNAstar FastA

libGenome

A cross platform C++ development library to manipulate DNA and protein sequences. It can read and write sequence and annotation data in several file formats.

genome rearrangement inversion locator large-scale recombination

GRIL	GRIL automates the process of identifying large-scale genome inversions and rearrangements

Genome Retrieval

GRS	A Graphic Tool for Genome Retrieval and Segment Analysis

Genomes

GenomePixelizer

Genome Visualization Tool: Detection of duplicating events in genomes, Displaying the Genetic Maps, Comparative genetics in general.

genomic annotation

gff2ps

Converting genomic annotations in GFF format to PostScript

genomic database system

Acedb

Acedb is a genome database system originally developed for the C.elegans genome project

genomics

Clann	Clann: 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
PyPhy	PyPhy is a set of python scripts and modules for automatic, large-scale reconstructions of phylogenetic relationships of complete microbial genomes.

GFF

gff2ps

Converting genomic annotations in GFF format to PostScript

global fitting

UltraScan

UltraScan is a comprehensive GUI editing and data analysis package for hydrodynamic data from analytical ultracentrifugation experiments

gotoh's improvement

Graph theory

PhyloGrapher

grep

Biogrep

A grep that is optimized for biosequences. Biogrep is designed to locate large sets of patterns in sequence databases in parallel.

group-specific

Amplicon

Program for designing group-specific PCR primer sets

Hidden Markov Models

HMMER	Profile hidden Markov models for biological sequence analysis
SAM equence Alignment and Modeling Syste	a collection of flexible software tools for creating, refining, and using linear hidden Markov models for biological sequence analysis

HMM

VEIL	A hidden Markov model for finding genes in vertebrate DNA�

homologous genes

PhyloGrapher

inference

MOLPHY	A Computer Program Package for Molecular Phylogenetics including ProtML
PHASE	PHASE 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.

java

Artemis	a 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.
BioJava	The BioJava Project is an open-source project dedicated to providing Java tools for processing biological data.
MAExplorer	The 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.

library

Friend	Friend, an Integrated Front-end Application for Bioinformatics
libGenome	A cross platform C++ development library to manipulate DNA and protein sequences. It can read and write sequence and annotation data in several file formats.

maximum likelihood

fastDNAml	Estimates maximum likelihood phylogenetic trees from nucleotide sequences
MOLPHY	A Computer Program Package for Molecular Phylogenetics including ProtML
PAML	Phylogenetic Analysis by Maximum Likelihood
TREE-PUZZLE:	TREE-PUZZLE: Maximum likelihood analysis for nucleotide, amino acid, and two-state data

Maximum likelihood analysis

TREE-PUZZLE:

TREE-PUZZLE: Maximum likelihood analysis for nucleotide, amino acid, and two-state data

Maximum Likelihood Inference of Protein Phylogeny

MOLPHY

A Computer Program Package for Molecular Phylogenetics including ProtML

maximum likelihood phylogenetic trees

fastDNAml

Estimates maximum likelihood phylogenetic trees from nucleotide sequences

MCMC

PHASE

PHASE 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.

medline

BioMail

automate searching for recent scientific papers in the PubMed Medline database

melting temperature

MELTING

Accurate computation of the enthalpy, entropie and melting temperature of a nucleic acid duplex

microarray

MAExplorer	The 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.
SEPON	SEPON 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
Teiresias-based Gene expression analysis	Discover patterns in microarray data using the Teiresias algorithm. Allows discovery of inversely regulated genes.

microarray analysis

MAExplorer	The 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.
Teiresias-based Gene expression analysis	Discover patterns in microarray data using the Teiresias algorithm. Allows discovery of inversely regulated genes.

microarray analysis software

MAExplorer

The 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.

modeling

AMMP	a modern full-featured molecular mechanics, dynamics and modeling program.
Kintecus	Run chemical kinetics/fitting of catalyst reactor, and enzyme reactions
MMTK-2.2	molecular modeling tool-kit 2.2
Oslet	A molecular modeling and simulation environment in Java, mainly for education.
WHAT IF	WHAT IF is a versatile protein structure analysis program that can be used for mutant prediction, structure verification, molecular graphics, etc

Molecular Dynamics high performance simulator

Gromacs

The World' s fastest Molecular Dynamics - and it' s gpl

molecular dynamics modeling pdb force field

MMTK-2.2

molecular modeling tool-kit 2.2

molecular dynamics simulations

GDIS	a GTK based program for the display and manipulation of isolated molecules and periodic systems

molecular editor

PyMol

PyMOL 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.

molecular graphics

Chimera	Excellent 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
Oslet	A molecular modeling and simulation environment in Java, mainly for education.
Spock	a full-featured molecular graphics program

molecular mechanics

AMMP	a modern full-featured molecular mechanics, dynamics and modeling program.

molecular modeling

Oslet	A molecular modeling and simulation environment in Java, mainly for education.
WHAT IF	WHAT IF is a versatile protein structure analysis program that can be used for mutant prediction, structure verification, molecular graphics, etc

molecular modelling

Babel

a program designed to interconvert a number of file formats currently used in molecular modeling

molecular rendering

Garlic

a free molecular visualization program

molecular simulations

Oslet

A molecular modeling and simulation environment in Java, mainly for education.

molecular structure analysis

Chimera

Excellent 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

molecular visualization

Garlic	a free molecular visualization program
rasmol	RasMol is a free program which displays molecular structure.
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
VMD	VMD is a molecular visualization program for displaying, animating, and analyzing large biomolecular systems using 3-D graphics and built-in scripting

molecular visualization program

Garlic

a free molecular visualization program

molecular weight

XMolCalc

a small utility that allows you to calculate a molecular weight

monte carlo

UltraScan

UltraScan is a comprehensive GUI editing and data analysis package for hydrodynamic data from analytical ultracentrifugation experiments

motif

Biogrep	A grep that is optimized for biosequences. Biogrep is designed to locate large sets of patterns in sequence databases in parallel.
RNABOB	RNABOB -- fast RNA motif/pattern searcher

MPI

mpiBLAST

mpiBLAST is a parallel implementation of NCBI-BLAST that uses database segmentation. It achieves a super-linear speedup in some cases.

multiple

Chimera	Excellent 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
clustalw	The famous ClustalW multiple alignment program
clustalx	Clustal X provides a window-based user interface to the ClustalW multiple alignment program
DCSE	DCSE (Dedicated Comparative Sequence Editor) is a multiple alignment editor
Friend	Friend, an Integrated Front-end Application for Bioinformatics
Jalview	Jalview - a java multiple alignment editor
Mauve	Mauve is a multiple genome alignment and visualization package that considers large-scale rearrangements in addition to nucleotide substitution and indels.
ModView	ModView is a program to visualize and analyze multiple biomolecule structures and/or sequence alignments.
Musca	Multiple sequence alignment of aa or nucleotide sequences / uses pattern discovery
MUSCLE	Multiple sequence alignment. More accurate than T-Coffee, faster than CLUSTALW.
seaview	SeaView is a graphical multiple sequence alignment editor
ShadyBox.	ShadyBox. The FIRST GUI based WYSIWYG multiple sequence alignment drawing program for Major Unix platforms

multiple alignment editor

DCSE	DCSE (Dedicated Comparative Sequence Editor) is a multiple alignment editor
Jalview	Jalview - a java multiple alignment editor
ModView	ModView is a program to visualize and analyze multiple biomolecule structures and/or sequence alignments.

multiple genome alignment comparison rearrangement

Mauve

Mauve is a multiple genome alignment and visualization package that considers large-scale rearrangements in addition to nucleotide substitution and indels.

multiple protein structure visualization

ModView

ModView is a program to visualize and analyze multiple biomolecule structures and/or sequence alignments.

multiple sequence alignment

Chimera	Excellent 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
clustalw	The famous ClustalW multiple alignment program
clustalx	Clustal X provides a window-based user interface to the ClustalW multiple alignment program
ModView	ModView is a program to visualize and analyze multiple biomolecule structures and/or sequence alignments.
Musca	Multiple sequence alignment of aa or nucleotide sequences / uses pattern discovery
MUSCLE	Multiple sequence alignment. More accurate than T-Coffee, faster than CLUSTALW.
seaview	SeaView is a graphical multiple sequence alignment editor
ShadyBox.	ShadyBox. The FIRST GUI based WYSIWYG multiple sequence alignment drawing program for Major Unix platforms

multiple sequence alignment analys is

Chimera

multiple sequence alignment drawing program

ShadyBox.

ShadyBox. The FIRST GUI based WYSIWYG multiple sequence alignment drawing program for Major Unix platforms

mysql

Ensembl

software system which produces and maintains automatic annotation on eukaryoticgenomes

NAMD

NAMD	NAMD is a parallel, object-oriented molecular dynamics code designed for high-performance simulation of large biomolecular systems.

neural networks

LIBELLULA

LIBELLULA is a neural network based web server to evaluate fold recognition results

neural net

RNA GENiE

A web based program for the prediction of rna genes in genomic DNA sequences

nmr

CNS	The 'Crystallography & NMR System' for macromolecular structure anaylsis

nucleic acid

MELTING

Accurate computation of the enthalpy, entropie and melting temperature of a nucleic acid duplex

oligonucleotide

Amplicon	Program for designing group-specific PCR primer sets
SEPON	SEPON 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

online searching

MPSRCH

MPSRCH (tm) is a suite of Smith-Waterman sequence analysis programs which run under Linux and Tru64 on Intel and Alpha.

online tools

On-line Genome Annotations

Annotations for many eukaryotic, bacterial and archaeal genomes. Can be searched using accession numbers or sought features

parallel

mpiBLAST

mpiBLAST is a parallel implementation of NCBI-BLAST that uses database segmentation. It achieves a super-linear speedup in some cases.

pattern

Biogrep	A grep that is optimized for biosequences. Biogrep is designed to locate large sets of patterns in sequence databases in parallel.
Musca	Multiple sequence alignment of aa or nucleotide sequences / uses pattern discovery
PatScan	PatScan is a pattern matcher which searches protein or nucleotide (DNA, RNA, tRNA etc.) sequence archives for instances of a pattern which you input
Pratt	a pattern discovery tool

pattern discovery

Musca

Multiple sequence alignment of aa or nucleotide sequences / uses pattern discovery

pattern matcher

PatScan

PatScan is a pattern matcher which searches protein or nucleotide (DNA, RNA, tRNA etc.) sequence archives for instances of a pattern which you input

pattern matching

Biogrep

A grep that is optimized for biosequences. Biogrep is designed to locate large sets of patterns in sequence databases in parallel.

PCR

Amplicon

Program for designing group-specific PCR primer sets

PDB

Garlic	a free molecular visualization program
MMTK-2.2	molecular modeling tool-kit 2.2

perl

GEANFAMMER

GEnome ANalysis and Protein FAMily MakER

Phase

PHASE

phenotype analysis

Teiresias-based Association Discovery

Discover associations in your data set (gene expression analysis, phenotype analysis, etc.)

phylogenetic

ATV	a phylogenetic tree display tool
fastDNAml	Estimates maximum likelihood phylogenetic trees from nucleotide sequences
njplot	NJplot is a tree drawing program able to draw any binary tree expressed in the standard phylogenetic tree format
PAML	Phylogenetic Analysis by Maximum Likelihood
Paup	Software package for inference of evolutionary trees
PHASE	PHASE 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.
PHYLIP	PHYLIP 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
phylowin	Phylo_win is a graphical colour interface for molecular phylogenetic inference.
PyPhy	PyPhy is a set of python scripts and modules for automatic, large-scale reconstructions of phylogenetic relationships of complete microbial genomes.
unrooted	Unrooted 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.

phylogenetic tree

ATV	a phylogenetic tree display tool
fastDNAml	Estimates maximum likelihood phylogenetic trees from nucleotide sequences
njplot	NJplot is a tree drawing program able to draw any binary tree expressed in the standard phylogenetic tree format
PAML	Phylogenetic Analysis by Maximum Likelihood
Paup	Software package for inference of evolutionary trees
PHYLIP	PHYLIP 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
phylowin	Phylo_win is a graphical colour interface for molecular phylogenetic inference.
PyPhy	PyPhy is a set of python scripts and modules for automatic, large-scale reconstructions of phylogenetic relationships of complete microbial genomes.
unrooted	Unrooted 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.

Phylogenetic tree reconstruction

PAML	Phylogenetic Analysis by Maximum Likelihood

phylogenetic trees

ATV	a phylogenetic tree display tool
fastDNAml	Estimates maximum likelihood phylogenetic trees from nucleotide sequences
njplot	NJplot is a tree drawing program able to draw any binary tree expressed in the standard phylogenetic tree format
Paup	Software package for inference of evolutionary trees
PHYLIP	PHYLIP is a free package of programs for inferring phylogenies.
phylowin	Phylo_win is a graphical colour interface for molecular phylogenetic inference.
PyPhy	PyPhy is a set of python scripts and modules for automatic, large-scale reconstructions of phylogenetic relationships of complete microbial genomes.
unrooted	Unrooted 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.

phylogenomics

Clann	Clann: 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
PyPhy	PyPhy is a set of python scripts and modules for automatic, large-scale reconstructions of phylogenetic relationships of complete microbial genomes.

Phylogenomics phylogeny tree supertree genomic

Clann

Clann: 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

Phylogeny

Clann	Clann: 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
Friend	Friend, an Integrated Front-end Application for Bioinformatics
MOLPHY	A Computer Program Package for Molecular Phylogenetics including ProtML
PHASE	PHASE 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.
PhyloGrapher	PhyloGrapher 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.

PostScript

gff2ps

Converting genomic annotations in GFF format to PostScript

POV-Ray scenes

Deep View Swiss-PdbViewer

Swiss-PdbViewer is an application that provides a user friendly interface allowing to analyse several proteins at the same time

prediction

caRNAc	RNA secondary structure inference for set of homologous sequences
ConsInspector	A tool for the prediction of protein binding sites in nucleic acids
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.
LIBELLULA	LIBELLULA is a neural network based web server to evaluate fold recognition results

primer

Amplicon	Program for designing group-specific PCR primer sets
primer	a program for picking primers for PCR reaction

primer selection

primer

a program for picking primers for PCR reaction

program

DIALIGN	DIALIGN is an alignment program that relies on comparison of whole segments of the sequences instead of comparison of single residue
Garlic	a free molecular visualization program
PHASE	PHASE 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.
ShadyBox.	ShadyBox. The FIRST GUI based WYSIWYG multiple sequence alignment drawing program for Major Unix platforms

PROSITE

ProSA

ProSA is a useful web application for finding known protein domains in nucleotide/protein sequences via PROSITE database searching

protein binding sites

ConsInspector

A tool for the prediction of protein binding sites in nucleic acids

protein docking

ZDOCK

Protein-protein complex structure prediction software

protein domains

DomainFinder	DomainFinder 1.0 DomainFinder is an interactive program for the determination and characterization of dynamical domains in proteins
ProSA	ProSA is a useful web application for finding known protein domains in nucleotide/protein sequences via PROSITE database searching

protein families

GEANFAMMER

GEnome ANalysis and Protein FAMily MakER

protein interaction

ZDOCK

Protein-protein complex structure prediction software

protein modelling

BRAGI

BRAGI 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

protein structure

Abacus	ABaCUS is a no-frills program developed to investigate the significance of the putative correspondence between exons and units of protein structure.
Garlic	a free molecular visualization program
LIBELLULA	LIBELLULA is a neural network based web server to evaluate fold recognition results
MODELLER	a program for homology protein structure modelling by satisfaction of spatial restraints.
ModView	ModView is a program to visualize and analyze multiple biomolecule structures and/or sequence alignments.

protein structure modelling

MODELLER

a program for homology protein structure modelling by satisfaction of spatial restraints.

protein structure prediction

LIBELLULA

LIBELLULA is a neural network based web server to evaluate fold recognition results

protein/DNA/RNA family clustering

ModView

ModView is a program to visualize and analyze multiple biomolecule structures and/or sequence alignments.

pubmed

BioMail

automate searching for recent scientific papers in the PubMed Medline database

python

Biopython	The Biopython Project is an international association of developers of freely available Python tools for computational molecular biology.
PyPhy	PyPhy is a set of python scripts and modules for automatic, large-scale reconstructions of phylogenetic relationships of complete microbial genomes.

real-time visualization

PyMol

PyMOL 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.

reannotation

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.

regex

Biogrep

A grep that is optimized for biosequences. Biogrep is designed to locate large sets of patterns in sequence databases in parallel.

regular expression

Biogrep

A grep that is optimized for biosequences. Biogrep is designed to locate large sets of patterns in sequence databases in parallel.

regulatory sequence analysis

Toucan

A Java tool for regulatory sequence analysis: detecting over-represented motifs and modules in sets of co-regulated genes.

rendered animations

GDIS	a GTK based program for the display and manipulation of isolated molecules and periodic systems

RNA

caRNAc	RNA secondary structure inference for set of homologous sequences
caRNAsta	Comparative Analysis of RNA structures by Tree Alignment
cove	COVE is an implementation of stochastic context free grammar methods for RNA sequence/structure analysis.
ModView	ModView is a program to visualize and analyze multiple biomolecule structures and/or sequence alignments.
NCRNASCAN	a structural RNA genefinder
PHASE	PHASE 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.
PKNOTS	RNA pseudoknot prediction
RNA GENiE	A web based program for the prediction of rna genes in genomic DNA sequences
RNABOB	RNABOB -- fast RNA motif/pattern searcher
RnaViz	a user-friendly, portable, GUI program for producing publication-quality secondary structure drawings of RNA molecules. Drawings
tRNAscan-SE	tRNA 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.
Vienna RNA Package	RNA Secondary Structure Prediction and Comparison

RNA folding

Vienna RNA Package

RNA Secondary Structure Prediction and Comparison

RNA gene finder

NCRNASCAN

a structural RNA genefinder

RNA motif

RNABOB

RNABOB -- fast RNA motif/pattern searcher

RNA pseudoknots

PKNOTS

RNA pseudoknot prediction

RNA secondary structure

caRNAsta	Comparative Analysis of RNA structures by Tree Alignment
cove	COVE is an implementation of stochastic context free grammar methods for RNA sequence/structure analysis.

RNA secondary structures

caRNAsta

Comparative Analysis of RNA structures by Tree Alignment

SCF

phrap	a program for assembling shotgun DNA sequence data
phred	Phred reads DNA sequencer trace data, calls bases, assigns quality values to the bases, and writes the base calls and quality values to output files.

secondary structure

caRNAsta	Comparative Analysis of RNA structures by Tree Alignment
cove	COVE is an implementation of stochastic context free grammar methods for RNA sequence/structure analysis.
RnaViz	a user-friendly, portable, GUI program for producing publication-quality secondary structure drawings of RNA molecules. Drawings

SEPON

sequence

ARB	Microbiologist's sequence database tool
Artemis	a 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.
autoseq	a small package of base calling software for ABI automated DNA sequencers
Biogrep	A grep that is optimized for biosequences. Biogrep is designed to locate large sets of patterns in sequence databases in parallel.
BioJava	The BioJava Project is an open-source project dedicated to providing Java tools for processing biological data.
Biopython	The Biopython Project is an international association of developers of freely available Python tools for computational molecular biology.
BioWish	Biowish is a C-extension for the Tcl/Tk scripting language
Blast	BLAST (Basic Local Alignment Search Tool) is a set of similarity search programs designed to explore all of the available sequence databases
Chimera	Excellent 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
clustalw	The famous ClustalW multiple alignment program
clustalx	Clustal X provides a window-based user interface to the ClustalW multiple alignment program
consed	A Unix-based Graphical Editor and Automated Finishing Program for Phrap Sequence Assemblies
DBWatcher	DBWatcher is a program handling periodic BLAST searches to find similarities to your own sequences.
DNA-GUI	DNA Graphical User Interface
EMBOSS	EMBOSS is a package of high-quality FREE Open Source software for sequence analysis.
Friend	Friend, an Integrated Front-end Application for Bioinformatics
gBioSeq	Biological sequence (ADN, protein) editor for GTK/Linux
Genpak	a set of small utilities written in ANSI C to manipulate DNA sequences in a Unix fashion, fit for combining within shell and cgi scripts
JAligner	JAligner is a Java implementation of biological sequence alignment algorithms.
libGenome	A cross platform C++ development library to manipulate DNA and protein sequences. It can read and write sequence and annotation data in several file formats.
ModView	ModView is a program to visualize and analyze multiple biomolecule structures and/or sequence alignments.
MPSRCH	MPSRCH (tm) is a suite of Smith-Waterman sequence analysis programs which run under Linux and Tru64 on Intel and Alpha.
Musca	Multiple sequence alignment of aa or nucleotide sequences / uses pattern discovery
MUSCLE	Multiple sequence alignment. More accurate than T-Coffee, faster than CLUSTALW.
NCRNASCAN	a structural RNA genefinder
PatScan	PatScan is a pattern matcher which searches protein or nucleotide (DNA, RNA, tRNA etc.) sequence archives for instances of a pattern which you input
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
PKNOTS	RNA pseudoknot prediction
Pratt	a pattern discovery tool
readseq	Reads and writes nucleic/protein sequences in various format
SAM equence Alignment and Modeling Syste	a collection of flexible software tools for creating, refining, and using linear hidden Markov models for biological sequence analysis
SEALS	SEALS (A System for Easy Analysis of Lots of Sequences) is a software package expressly designed for large-scale research projects in bioinformatics.
seaview	SeaView is a graphical multiple sequence alignment editor
SeqPup	SeqPup biological sequence editor and analysis program
ShadyBox.	ShadyBox. The FIRST GUI based WYSIWYG multiple sequence alignment drawing program for Major Unix platforms
sp2fasta	produce a file in FASTA format from one in SWISSPROTor EMBL flat file format
Toucan	A Java tool for regulatory sequence analysis: detecting over-represented motifs and modules in sets of co-regulated genes.
tRNAscan-SE	tRNA 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.
WU-Blast	Washington U. Blast

Sequence Alignment

Chimera	Excellent 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
clustalw	The famous ClustalW multiple alignment program
clustalx	Clustal X provides a window-based user interface to the ClustalW multiple alignment program
JAligner	JAligner is a Java implementation of biological sequence alignment algorithms.
ModView	ModView is a program to visualize and analyze multiple biomolecule structures and/or sequence alignments.
Musca	Multiple sequence alignment of aa or nucleotide sequences / uses pattern discovery
MUSCLE	Multiple sequence alignment. More accurate than T-Coffee, faster than CLUSTALW.
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
SAM equence Alignment and Modeling Syste	a collection of flexible software tools for creating, refining, and using linear hidden Markov models for biological sequence analysis
seaview	SeaView is a graphical multiple sequence alignment editor
ShadyBox.	ShadyBox. The FIRST GUI based WYSIWYG multiple sequence alignment drawing program for Major Unix platforms

sequence analysis

ARB	Microbiologist's sequence database tool
BioJava	The BioJava Project is an open-source project dedicated to providing Java tools for processing biological data.
Biopython	The Biopython Project is an international association of developers of freely available Python tools for computational molecular biology.
BioWish	Biowish is a C-extension for the Tcl/Tk scripting language
Blast	BLAST (Basic Local Alignment Search Tool) is a set of similarity search programs designed to explore all of the available sequence databases
clustalw	The famous ClustalW multiple alignment program
clustalx	Clustal X provides a window-based user interface to the ClustalW multiple alignment program
DNA-GUI	DNA Graphical User Interface
EMBOSS	EMBOSS is a package of high-quality FREE Open Source software for sequence analysis.
MPSRCH	MPSRCH (tm) is a suite of Smith-Waterman sequence analysis programs which run under Linux and Tru64 on Intel and Alpha.
NCRNASCAN	a structural RNA genefinder
PatScan	PatScan is a pattern matcher which searches protein or nucleotide (DNA, RNA, tRNA etc.) sequence archives for instances of a pattern which you input
PKNOTS	RNA pseudoknot prediction
Pratt	a pattern discovery tool
readseq	Reads and writes nucleic/protein sequences in various format
SEALS	SEALS (A System for Easy Analysis of Lots of Sequences) is a software package expressly designed for large-scale research projects in bioinformatics.
sp2fasta	produce a file in FASTA format from one in SWISSPROTor EMBL flat file format
Toucan	A Java tool for regulatory sequence analysis: detecting over-represented motifs and modules in sets of co-regulated genes.
tRNAscan-SE	tRNA 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.
WU-Blast	Washington U. Blast

sequence comparisons

DBWatcher

DBWatcher is a program handling periodic BLAST searches to find similarities to your own sequences.

sequence conversion

readseq	Reads and writes nucleic/protein sequences in various format
sp2fasta	produce a file in FASTA format from one in SWISSPROTor EMBL flat file format

sequence database

ARB	Microbiologist's sequence database tool

sequence editor

gBioSeq	Biological sequence (ADN, protein) editor for GTK/Linux
SeqPup	SeqPup biological sequence editor and analysis program

sequence finishing

consed

A Unix-based Graphical Editor and Automated Finishing Program for Phrap Sequence Assemblies

sequence patterns

Pratt

a pattern discovery tool

sequence similarity

Blast

BLAST (Basic Local Alignment Search Tool) is a set of similarity search programs designed to explore all of the available sequence databases

sequence utiities

Genpak

a set of small utilities written in ANSI C to manipulate DNA sequences in a Unix fashion, fit for combining within shell and cgi scripts

sequences

Friend

Friend, an Integrated Front-end Application for Bioinformatics

sequencing

autoseq	a small package of base calling software for ABI automated DNA sequencers
consed	A Unix-based Graphical Editor and Automated Finishing Program for Phrap Sequence Assemblies
phrap	a program for assembling shotgun DNA sequence data
phred	Phred reads DNA sequencer trace data, calls bases, assigns quality values to the bases, and writes the base calls and quality values to output files.

Smith-Waterman

JAligner	JAligner is a Java implementation of biological sequence alignment algorithms.
MPSRCH	MPSRCH (tm) is a suite of Smith-Waterman sequence analysis programs which run under Linux and Tru64 on Intel and Alpha.

Solid Angle calculation

Steric

A 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

staden

Staden Package

This 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.

statistic mechanics

Oslet

A molecular modeling and simulation environment in Java, mainly for education.

Steric Size calculation

Steric

A 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

structural alignments

Deep View Swiss-PdbViewer

Swiss-PdbViewer is an application that provides a user friendly interface allowing to analyse several proteins at the same time

structural biology

DINO	a realtime 3D visualization program for structural biology data.

structure

Abacus	ABaCUS is a no-frills program developed to investigate the significance of the putative correspondence between exons and units of protein structure.
caRNAc	RNA secondary structure inference for set of homologous sequences
caRNAsta	Comparative Analysis of RNA structures by Tree Alignment
Chimera	Excellent 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
CNS	The 'Crystallography & NMR System' for macromolecular structure anaylsis
cove	COVE is an implementation of stochastic context free grammar methods for RNA sequence/structure analysis.
Garlic	a free molecular visualization program
LIBELLULA	LIBELLULA is a neural network based web server to evaluate fold recognition results
MODELLER	a program for homology protein structure modelling by satisfaction of spatial restraints.
ModView	ModView is a program to visualize and analyze multiple biomolecule structures and/or sequence alignments.
MOPAC7	a general-purpose semi-empirical molecular orbital package for the study of chemical structures and reactions.
PyMol	PyMOL 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.
RNA GENiE	A web based program for the prediction of rna genes in genomic DNA sequences
RnaViz	a user-friendly, portable, GUI program for producing publication-quality secondary structure drawings of RNA molecules. Drawings

structure analysis

Chimera	Excellent 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
CNS	The 'Crystallography & NMR System' for macromolecular structure anaylsis

structure prediction

caRNAc	RNA secondary structure inference for set of homologous sequences
LIBELLULA	LIBELLULA is a neural network based web server to evaluate fold recognition results

stuctures

Friend

Friend, an Integrated Front-end Application for Bioinformatics

substitution

PAML	Phylogenetic Analysis by Maximum Likelihood
PHASE	PHASE 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.

substitution rates

PAML	Phylogenetic Analysis by Maximum Likelihood

swissprot

sp2fasta

produce a file in FASTA format from one in SWISSPROTor EMBL flat file format

Tcl/Tk

BioWish

Biowish is a C-extension for the Tcl/Tk scripting language

thermodynamics

caRNAc	RNA secondary structure inference for set of homologous sequences
MELTING	Accurate computation of the enthalpy, entropie and melting temperature of a nucleic acid duplex

threading

LIBELLULA

LIBELLULA is a neural network based web server to evaluate fold recognition results

trace

io_lib	An open source C library of sequence trace files supporting ABI, ALF, SCF, CTF and ZTR file formats.
phrap	a program for assembling shotgun DNA sequence data
phred	Phred reads DNA sequencer trace data, calls bases, assigns quality values to the bases, and writes the base calls and quality values to output files.
Staden Package	This 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.
UltraScan	UltraScan is a comprehensive GUI editing and data analysis package for hydrodynamic data from analytical ultracentrifugation experiments

trace chromatogram

io_lib

An open source C library of sequence trace files supporting ABI, ALF, SCF, CTF and ZTR file formats.

trace files

phrap	a program for assembling shotgun DNA sequence data
phred	Phred reads DNA sequencer trace data, calls bases, assigns quality values to the bases, and writes the base calls and quality values to output files.

trajectory analysis

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

transcription factor binding sites

GenomeInspector

Software for the analysis of spatial correlations of elements on DNA sequences

transcription factors

Toucan

A Java tool for regulatory sequence analysis: detecting over-represented motifs and modules in sets of co-regulated genes.

tree

ATV	a phylogenetic tree display tool
Clann	Clann: 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
fastDNAml	Estimates maximum likelihood phylogenetic trees from nucleotide sequences
Friend	Friend, an Integrated Front-end Application for Bioinformatics
njplot	NJplot is a tree drawing program able to draw any binary tree expressed in the standard phylogenetic tree format
PAML	Phylogenetic Analysis by Maximum Likelihood
Paup	Software package for inference of evolutionary trees
PHASE	PHASE 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.
PHYLIP	PHYLIP 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
phylowin	Phylo_win is a graphical colour interface for molecular phylogenetic inference.
PyPhy	PyPhy is a set of python scripts and modules for automatic, large-scale reconstructions of phylogenetic relationships of complete microbial genomes.
unrooted	Unrooted 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.

tree of life

PHASE

tree viewer

ATV	a phylogenetic tree display tool
njplot	NJplot is a tree drawing program able to draw any binary tree expressed in the standard phylogenetic tree format
phylowin	Phylo_win is a graphical colour interface for molecular phylogenetic inference.
unrooted	Unrooted 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.

tRNA searching

tRNAscan-SE

tRNA 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.

visualisation

Friend

Friend, an Integrated Front-end Application for Bioinformatics

visualization

Garlic	a free molecular visualization program
GeneView II	Interactive GenBank Entry Visualization
gff2ps	Converting genomic annotations in GFF format to PostScript
ModView	ModView is a program to visualize and analyze multiple biomolecule structures and/or sequence alignments.
PyMol	PyMOL 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.
rasmol	RasMol is a free program which displays molecular structure.
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
VMD	VMD is a molecular visualization program for displaying, animating, and analyzing large biomolecular systems using 3-D graphics and built-in scripting

VMD

NAMD	NAMD is a parallel, object-oriented molecular dynamics code designed for high-performance simulation of large biomolecular systems.

Web robots

Sight

Allows programming free assembling of web resoureces, local executables and ssh services into arbitrary workflow.

workflow

Sight

Allows programming free assembling of web resoureces, local executables and ssh services into arbitrary workflow.

xchange biological data

OmniGene

Standardizing Biological Data Interchange Through Web Services Technology

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 thomas@biopython.org or use the following form

Links²Go
Linux Software

Sicheritz-Ponten Thomas, Ph.D  CBS, Department of Biotechnology
thomas@biopython.org           The Technical University of Denmark
CBS:  +45 45 252485            Building 208, DK-2800 Lyngby
Fax   +45 45 931585            http://www.cbs.dtu.dk/thomas

        De Chelonian Mobile ... The Turtle Moves ...

Molecular Linux Molecular Biology related programs for Linux

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Molecular Linux
Molecular Biology related programs for Linux