Stothard Research Group

University of Alberta

Bioinformatics

NCBI

PubMed Nucleotide Protein Gene OMIM SNP UniGene

General Purpose

EMBOSS BioPerl BioJava BioPython BioRuby BCM Search Launcher Sequence Manipulation Suite Bioinformatics.org NCBI Genome Workbench Bioinformatics Links Directory BioMart The Synergizer Galaxy

Molecular Biology

Sequence Extractor PlasMapper Primer-BLAST SNPbox

Sequence Processing

phred Lucy RepeatMasker Repbase SeqClean TGICL CD-HIT ESTScan MIRA AMOS

Annotated Genomes

Ensembl UCSC Genome Browser HAMAP WormBase FlyBase ZFIN SGD

Searching and Alignment

BLAST HMMER Pfam ClustalW mpiBLAST MUMmer SyntenyMiner Artemis Comparison Tool Jalview exonerate SSAHA ssahaSNP PyroBayes Sputnik PASA ALIGN0 HHpred

Short Read Analysis

SOAP GMAP Maq SHRIMP RMAP PbShort Slider Tagger Vancouver Short Read Analysis Package Velvet MetaSim SOLiD Software Development Community CloudBurst SCARF Erange SAMtools TopHat Cufflinks Genome Sequencing and Analysis Group

Sequence Annotation

Manatee Artemis Pirate GO GenDB Blast2GO SEED MEME InterProScan UniProt Inparanoid EST2uni

Microbial Ecology

Ribosomal Database Project ARB greengenes cpnDB UniFrac STAP MEGAN ShotgunFunctionalizeR PhyloPythia CARMA MG-RAST mothur RAMMCAP QIIME

Microbial Genomics

CMR BacMap BacMap (mirror) BASys EcoCyc CGView CGView Server Circos

Pathways and Interactions

KEGG DIP IntAct Cytoscape

Gene Expression

TIGR MeV Bioconductor FatiGO limmaGUI GenePattern DAVID FuncAssociate

Phylogenetics

PAML PHYLIP Dendroscope Mesquite MrBayes T-REX NJplot Berkeley Phylogenomics Group Phylogeny.fr MEGA

Gene Association and QTL Mapping

PLINK QTL Express QTL Cartographer

Programming

Operating Systems

Linux Online Red Hat Fedora Debian Ubuntu Bio-Linux

Guides

Linux Bash Subversion CVS Emacs Shell scripts Vi Request tracker PLINK

Documentation

CentOS 5 Apache HTTP Server MySQL Java Perl PHP JavaScript XHTML Red Hat Linux manuals CSS StatSoft Electronic Textbook GraphPad Prism Sun Grid Engine SAS Documentation

Development Tools

Eclipse Hibernate Subversion Ruby on Rails TurboGears Catalyst Checkstyle VMware Xen Spring ICEfaces RStudio

More Software
Computing Clusters

Rocks Clusters Grid Engine MPI ScaLAPACK CentOS

Mac OS X

Fink

Other

Information

Google Google Maps Canada Yahoo bing Wikipedia Wolfram|Alpha Dictionary.com

News

CBC BBC CNN Reuters Slashdot reddit Twitter

Music

Aphex Twin FAX Boards of Canada Banco de Gaia Ulrich Schnauss Discogs

Photo and Video

Photo.net Digital Photography Review Flickr Panoramio Vimeo YouTube AVS Forum

Video Games

Classic Gaming Arcade@home IGN 1UP.COM GameSpot GameSpy

Weather

Edmonton, Alberta Calgary, Alberta Victoria, British Columbia Quebec, Quebec Toronto, Ontario London, United Kingdom Seoul, South Korea Singapore, Singapore

Maps

University of Alberta (Google Maps) University of Alberta (PDF) Edmonton International Airport (Google Maps) Victoria, BC (Google Maps)

Financial

TSX Group NYSE Group

Edmonton

craigslist edmonton Kijiji Edmonton Edmonton Restaurant Reviews Edmonton Movie Guide

University of Alberta

Academic Calendar Administrative Information Systems Research Services Office Supply Management Services Financial Services Human Resource Services

Miscellaneous

Cycles Marinoni Rocky Mountain Bicycles Pure Design Royal Canadian Mint eBay Amazon.com MonoPrice.com GuerrillaMail.com drobo

Journals

Nature Science PLoS Biology PLoS Computational Biology Nucleic Acids Research Bioinformatics BMC Bioinformatics BioEssays

Lab Internal

Stothard Group server Stothard Group homepage Cluster status Storage