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Web Resources for Molecular Biology (2007) Free software BioEdit Sequence Alignment Editor for Windows... Biolinux [ Home ] bioperl.org - Main page Digital Taxonomy - Software EBI Downloads EBI's software archive EMBOSS Homepage Filter DNA Genamics SoftwareSeek GeneDoc HomePage IUBio Archive for Biology mekentosj.com _ Li[vf]e at Neefix Laboratories Molecular Genetics Jump Station Oxford Evolutionary Biology - Se-Al PhyML - aLRT Scientific Applications on Linux (SAL) SeWeR_Home The BUGS Project - Bayesian inference Using Gibbs Sampling University of Dundee - Geoff Barton Bioinformatics and Computational Biology Research Group Vector NTI - User Community General online analyses Biological software at the Inst. Pasteur EBI Services EMBnet Norway EMBOSS explorer EMBnet Swiss web access to EMBOSS via wEMBOSS ExPASy Molecular Biology Server Readseq - biosequence conversion tool SDSC Biology Workbench SDSC Projects Swiss EMBnet node server Welcome to EMBnet_CNB Genome Resources Genome Browsers and annotation Apollo Genome Annotation Curation Tool Argo Genome Browser ECR Browser GBrowse_ The Generic Genome Browser _ GMOD Genome Browser Informatics Software_ Artemis UCSC Genome Browser Home UT Genome Browser (Medaka) Vista tools Human and other mammalian CardioGenomics_ Homepage euGenes_ Eukaryote Genes GeneCards Homepage Human BLAT Search Human Genome Browser Gateway K-BROWSER v1.0 Microarray Databases and Tools MINT database The Genome Database The Human Gene Mutation Database (HGMD) Vega Genome Browser non-mammalian Saccharomyces Genome Database Stanford Genomic Resources STDGEN Databases The Sanger Institute_ Microbes TIGR Databases - The Institute for Genomic Re... Vega Zebrafish (Danio rerio) Virus Database VIDA Ensembl Genome Browser GBrowse_ The Generic Genome Browser _ GMOD GenMAPP - Home Page Genome biology GOLD_ Genomes OnLine Database Homepage IMG Home Main Page - GMOD PathVisio - PathVisio Wiki SourceForge.net_ Mauve Vista tools Major Database sites BCM Human Transcript Database Home Page BIND - The Biomolecular Interaction Network DIP_Home ExPASy Databases Gene Regulation Genelynx Genome Portals GOLD_ Genomes OnLine Database Homepage Human Protein Reference Database Integrated Taxonomic Information System NCBI databases Official REBASE Homepage Oxford Journals _ Life Sciences _ Nucleic Acids Research _ Database Summary Paper Categories Pfam_ Pfam Home Page Protein Information Resource Home Page - Prot... RCSB Protein Data Bank TRANSFAC - The Transcription Factor Database Mass Spec Matrix Science - Home OMSSA ms_ms search engine SEQUEST Home Page Microarray_stuff_2006 Commercial software Agilent _ GeneSpring GX BioDiscovery Microarray Analysis Software and Services __ GeneSight GeneMaths XT - Microarray Analysis Software Integrated Genomics Microarray analysis software solution - SilicoCyte Partek - Statistical Analysis & Interactive Visualization Software Rosetta Biosoftware Resolver R The Comprehensive R Archive Network Welcome to Bioconductor — bioconductor.org An (Opinionated) Guide to Microarray Data Analysis Asterias Bayesian Analysis of Variance for Microarrays Biometric Research Branch home page Brown Lab Homepage caBIG - Welcome to the caBIG™ Web site caGEDA_ A web application for the integrated analysis of global gene expression patterns in can Cleaver Home dChip Software (DNA-Chip Analyzer) DNA Microarray (Genome Chip) (by Leming Shi, ... EBI Tools - Expression Profiler Home ENGENE - DNA array Data Processing and Exploratory Data Analysis Gene Expression Omnibus Home GenePattern GenMAPP - Home Page GEOSS_ Gene Expression Open Source System Home - Workbench Laboratory for the analysis of microarray data_ Main page Links to microarray tools, data, methods (Jaa... Mark Fontenot - Microarray Software List MGED - Microarray Gene Expression Databases G... MIAME Microarray data mining software (comprehensive software) MicroArray Explorer - MAExplorer Molecular Informatics Resource for the Analys... NCICB GForge_ Software Map SNOMAD - Standardization and NOrmalization of MicroArray Data Software - The Jackson Laboratory StatWeb_ Statistical Microarray Data Analysis The Pevsner Laboratory TM4_ MeV Welcome to Cyber-T Molecular Systematics Bosque_ Phylogenetic Trees Drawing Tool Inferring Phylogenies - Sinauer Associates, Inc. iTOL_ Interactive Tree Of Life MacClade 4_ Analysis of Phylogeny and Character Evolution - Sinauer Associates, Inc. MacClade Home Page mcope - minimum conflict phylogeny estimation PAL_ Phylogenetic Analysis Library PAUP_ 4.0 PAUP__ Phylogenetic Analysis Using Parsimony (and Other Methods) 4.0 Beta - Sinauer Associates, PHYLIP Home Page PHYLIP primer Phylodendron PhyloDraw is a drawing tool for creating phylogenetic trees. Phylogenetics Glossary PHYML_ fast, accurate estimation of large PHYlogenies by Maximum Likelihood The Tree of Life Home Page TREE-PUZZLE TreeView t_coffee home page Webpage of James O. McInerney, head of the BioiÉ WebPhylip Phylogenetics resources Computational Phylogenetics at SC98 Glossary of Phylogenetic Systematics Journey into the World of Cladistics Likelihood-Based Tests of Topologies in Phylo... Molecular phylogenetics Phylogenetic Analysis of Proteins Phylogenetics Glossary Phylogenetics Publications Phylogenetics Resources Phylogenetics Phylogenetics_ Introduction PHYML_ fast, accurate estimation of large PHYlogenies by Maximum Likelihood PPS 96' - Molecular Phylogenetics SASB Introduction to Phylogenetics The Mathematical Basis of Molecular Phylogene... The Tree of Life Home Page TreeBASE Welcome to the Molecular Systematics homepage. Primer design GeneFisher - Interactive PCR Primer Design Genome Sequence Centre - AcePrimer PCR Primer Design Primer Design Primer3 Input $CGI_VERSION Primer3 Input (primer3.cgi v 0.2c) Web Primer_ DNA and Purpose Entry programming and scripting BioPERL PERL course CodeWarriorU.com MacPerl RAP's Home Page The Perl Language Home Page www.perl.com - O'Reilly's Bioch508 - Syllabus Bioperl course Bioperl OSX installation bioperl.org - Latest Distribution bioperl.org - Main page BioPerlTutorial - a tutorial for bioperl Open Bioinformatics Foundation Perl modules documentation for bioperl-1.2 Perl Tutorial Canadian Bioinformatics Help Desk -- Software Repository -- Table View Friend page http___biopython.org_ Protein structure prediction BCM Search Launcher_ Protein Secondary Struct... EMBL Dali_ email server for 3-D protein struc... HMMSTR_ROSETTA Server Jpred - Submission Form Modeller. Ple BioInformatique Lyonnais - Lyon - Gerland Predicting the Secondary Structure of Your Pr... PredictProtein_ structure prediction and sequ... Protein secondary structure prediction Protein Structure Databases and Search Tools Protein Structure Prediction Center Protein Structure Prediction Protein Structure PSIPRED_ a protein structure prediction server SWISS-MODEL The RCSB Protein Data Bank Search engines and URL lists repeat finders http___www.girinst.org_censor_index.php RepeatMasker at EMBL RepeatMasker Web Server 123 Genomics AlltheWeb.com Ask.com Search Engine - Better Web Search BioExchange.com Tools - Genomics and Bioinformatics Tools, Biology Resources, Protocols BIOINFORMATICS RESOURCES bioWWW CMS Molecular Biology Resource EvoPrinter - Introduction Genamics Home Google Harvard Dept of MCB - Biology Links Molecular Biology Freeware for Windows Molecular Biology Places of Interest ONLINE ANALYSIS TOOLS www.molbiol.net Sequence alignment BCM Search Launcher_ Multiple Sequence Alignm... CBRG_ Services - MultiAlign CLUSTALW (origin2) Clustalw Multalin interface page NEE-HOW_ software online- Sequence Alignment NPS@_ Welcome to Network Protein Sequence @na... Se-Al Sequence Alignment Editor T-Coffee Tcoffee The USC Sequence Alignment Server t_coffee home page VSNS BioComputing Division Multiple Alignment... Sequence searching BLAST_&_FASTA Blast Servers and Searches BLAST Blastall Batch Utility - Blast Command Generator DNA Data Bank of Japan WWW Title Page FASTA Programs Fasta III. STRATEGIES FOR FINDING DISTANT SIMILARITIES Links to external Blast servers NCBI BLAST Home Page Sequence searches Sequence Similarity Search - FASTA SWBIC - Batch BLAST The Sanger Centre _ Database Search Services The Statistics of Sequence Similarity Scores USDA Bioinformatics Coordination Program for Animal Genome SRS on the web SRS resource pages SRS HELP SRSWWW at EMBL, Heidelberg SRSWWW at EMBL-EBI, Hinxton, Cambridge, UK SRS SRS6 GenomeNet WWW server My NCBI Quick Tours PAPIA _ PArallel Protein Information Analysis system PubMed_ My NCBI Sequence Similarity Search - BLAST Sequence Similarity Search - FASTA The Sanger Institute _ Data Search Welcome to the BCM Search Launcher Specialized analysis sites Protein structure prediction EMBL Dali_ email server for 3-D protein struc... ExPASy - Tools HMM-based sequence query, Target99 Ple BioInformatique Lyonnais - Lyon - Gerland Predicting the Secondary Structure of Your Pr... PredictProtein - Structure Prediction and Sequence Analysis Protein Structure Databases and Search Tools Protein Structure Prediction Center Protein Structure Prediction SWISS-MODEL The PSIPRED protein structure prediction server The RCSB Protein Data Bank remote homology searching ISMB99 Tutorial Material Making the most of y... Profile hidden Markov models UCSC HMM Applications Main Page repeat finders http___www.girinst.org_censor_index.php RepeatMasker at EMBL RepeatMasker Web Server Sequence alignment BCM Search Launcher_ Multiple Sequence Alignments Clustalw LAGAN - Home NPS@_ Welcome to Network Protein Sequence @na... T-COFFEE server The USC Sequence Alignment Server USC Comp Bio Software VSNS BioComputing Division Multiple Alignment... Transcription factor & Promotor search Bayesian Bioinformatics at Wadsworth Center BIOBASE Biological Databases_ Home Gibbs Sampling for nucleotide sequences McPromoter promoter prediction server Scansite Menu Software from the Computational Molecular Bio... TESS _ Transcription Element Search System The BUGS Project - Bayesian inference Using G... The Gibbs Motif Sampler Homepage TRES_ A Tool for Comparative Promoter Sequenc... YMF 3.0 - Software for Finding DNA Motifs Bayesian Bioinformatics BoxShade Server CINEMA CloneIt Online GPCRDB home page HMMSTR_ROSETTA Server NetPhos 2.0 Server Trans_Promotor_analysis Bayesian Bioinformatics at Wadsworth Center Genomatix_ PromoterInspector Input form Gibbs Sampling for nucleotide sequences McPromoter promoter prediction server Molecular Informatics Resource for the Analys... Software from the Computational Molecular Bio... The BUGS Project - Bayesian inference Using G... The Gibbs Motif Sampler Homepage TRANSFAC - The Transcription Factor Database TRES_ A Tool for Comparative Promoter Sequenc... Welcome to TESS_ Transcription Element Search... Wyeth Wasserman CGB Home EMBL - Basic Research in Molecular Biology European Bioinformatics Institute ExPASy Molecular Biology Server genome.gov _ National Human Genome Research Institute http___igweb.integratedgenomics.com_GOLD_ ITC-ACHS Homepage Locating SNPs in a Gene or in Genes NCBI HomePage The Institute for Genomic Research The Wellcome Trust Sanger Institute