What are the best linux software for molecular biology?

Similar Questions: linux software molecular biology Recent Questions About: linux software molecular biology.

I'm simply providing a list of helpful links: These links contains lists of software, some including brief descriptions. bioinformatics.org/software/index.php3 pasteur.fr/cgi-bin/biology/bnb_s.pl?engl... usinglinux.org/biology/ dmoz.org/Science/Biology/Biochemistry_an... freshmeat.net/search/?q=molecular+biolog... .

There is a list of the best linux software for molecular biology. Molecular Biology related programs for Linux:Abacus ABaCUS is a no-frills program developed to investigate the significance of the putative correspondence between exons and units of protein structure. Biolisp BioLisp.org is a public resource supporting scientists who use Lisp to develop intelligent applications in the biological sciences.

BioMail automate searching for recent scientific papers in the PubMed Medline database Bioperl open source Perl tools for bioinformatics, genomics and life science research 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 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. 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 oneClann 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 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 consed A Unix-based Graphical Editor and Automated Finishing Program for Phrap Sequence Assemblies ConsInspector A tool for the prediction of protein binding sites in nucleic acids cove COVE is an implementation of stochastic context free grammar methods for RNA sequence/structure analysis. DBWatcher DBWatcher is a program handling periodic BLAST searches to find similarities to your own sequences.

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 DINO a realtime 3D visualization program for structural biology data. DNA-GUI DNA Graphical User Interface DomainFinder DomainFinder 1.0 DomainFinder is an interactive program for the determination and characterization of dynamical domains in proteins EMBOSS EMBOSS is a package of high-quality FREE Open Source software for sequence analysis. Ensembl software system which produces and maintains automatic annotation on eukaryoticgenomes fastDNAml Estimates maximum likelihood phylogenetic trees from nucleotide sequences Friend Friend, an Integrated Front-end Application for Bioinformatics Garlic a free molecular visualization program gBioSeq Biological sequence (ADN, protein) editor for GTK/Linux GDE The GDE is a set of programs for multiple sequence alignment and analysis.

GDIS a GTK based program for the display and manipulation of isolated molecules and periodic systems GEANFAMMER GEnome 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 II Interactive GenBank Entry Visualization GenomeInspector Software for the analysis of spatial correlations of elements on DNA sequenceslibGenome 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. 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.

Mauve Mauve is a multiple genome alignment and visualization package that considers large-scale rearrangements in addition to nucleotide substitution and indels. MELTING Accurate computation of the enthalpy, entropie and melting temperature of a nucleic acid duplex MeltSim Calculation of DNA melting curves and maps using the Poland-Scheraga algorithm and empirical constraints by R.D. Blake. MOPAC7 a general-purpose semi-empirical molecular orbital package for the study of chemical structures and reactions.

MpiBLAST mpiBLAST 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.

MSPcrunch a BLAST enhancement filter Musca Multiple sequence alignment of aa or nucleotide sequences / uses pattern discovery MUSCLE Multiple 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.

NCRNASCAN a structural RNA genefinder PAML Phylogenetic Analysis by Maximum Likelihood 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 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. 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.

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 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. Phylowin Phylo_win is a graphical colour interface for molecular phylogenetic inference. PKNOTS RNA pseudoknot prediction Populations Population genetic software (individuals or populations distances, phylogenetic trees) Pratt a pattern discovery tool primer a program for picking primers for PCR reaction ProSA ProSA is a useful web application for finding known protein domains in nucleotide/protein sequences via PROSITE database searching 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.

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 SeqPup SeqPup biological sequence editor and analysis program ShadyBox. ShadyBox.

The FIRST GUI based WYSIWYG multiple sequence alignment drawing program for Major Unix platforms Sight Allows programming free assembling of web resoureces, local executables and ssh services into arbitrary workflow. Sp2fasta produce a file in FASTA format from one in SWISSPROTor EMBL flat file format Spock a full-featured molecular graphics program 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.

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 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.

XMolCalc a small utility that allows you to calculate a molecular weight xsact EST clustering tool ZDOCK Protein-protein complex structure prediction software Sources: http://bioinformatics.org/software/index.php3 .

1 newbie850518, regarding your answer "There is a list of the best linux software for molecular biology. ": I asked which are the best. I could easily find the links you sent me (which I thank you the same for having proposed) but I would have liked an expert advice on the top 10 ones.

Thanks anyway,Escherian .

Newbie850518, regarding your answer "There is a list of the best linux software for molecular biology. ": I asked which are the best. I could easily find the links you sent me (which I thank you the same for having proposed) but I would have liked an expert advice on the top 10 ones.

Thanks anyway,Escherian.

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