Stothard Research Group

NCBI

PubMed Nucleotide Protein Gene OMIM OMIA SNP

General Purpose

EMBOSS BioPerl BioJava BioPython BioRuby Sequence Manipulation Suite Bioinformatics.org NCBI Genome Workbench BioMart The Synergizer Galaxy Staden Package UGENE

Molecular Biology

Sequence Extractor PlasMapper Primer-BLAST everyVECTOR ApE TraceTuner

Sequence Processing

RepeatMasker Repbase SeqClean TGICL CD-HIT ESTScan MIRA AMOS

Annotated Genomes

Ensembl UCSC Genome Browser HAMAP WormBase ZFIN SGD

Searching and Alignment

BLAST Pfam ClustalW MUSCLE T-Coffee mpiBLAST MUMmer SyntenyMiner Artemis Comparison Tool Jalview PASA HHpred

High-throughput Sequencing

ngopt SPAdes bwa GATK SAMtools snpEff SEQanswers BioStar IGV Tablet Trinity HISAT StringTie ballgown Picard Tools BBMap shovill

Sequence Assembly Quality Assessment

Sibelia QUAST Bandage

Sequence Annotation

Manatee Artemis Pirate Blast2GO SEED MEME InterProScan UniProt Inparanoid RAST Prokka

Microbial Ecology and Metagenomics

USEARCH/UPARSE/UCHIME LotuS QIIME 2 Ribosomal Database Project ARB MEGAN MG-RAST mothur Kraken EDGE STAMP

Microbial Genomics

KBase IMG/M BacMap BASys EcoCyc CGView CGView Server Circos CGView Comparison Tool SynTView

Pathways and Interactions

MetaCyc HUMAnN2 KEGG DIP IntAct Cytoscape

Gene Expression

WGCNA Bioconductor GenePattern DAVID FuncAssociate

Phylogenetics

REALPHY RAxML PAML iTOL PHYLIP Dendroscope MrBayes T-REX NJplot Phylogeny.fr MEGA FigTree

Gene Association and QTL Mapping

PLINK SNP2GO QTL Cartographer

Guides

Bash Shell scripts vi

Documentation

Apache HTTP Server MySQL StatSoft Electronic Textbook SAS Documentation

Development Tools

PyCharm Spyder Eclipse Ruby on Rails Catalyst Checkstyle ICEfaces RStudio

Virtual Machines and Containers

VMware Virtual Box Xen Docker Singularity

Computing Clusters

Rocks Clusters MPI ScaLAPACK Compute Canada Documentation

Reproducible Research

Project Jupyter R Markdown Conda Bioconda Snakemake Nextflow

Data Mining and Machine Learning

OpenRefine scikit-learn KNIME TensorFlow Keras Tableau

More Software
General Information

Google Google Maps Canada Yahoo bing Wikipedia Wolfram|Alpha

News

CBC BBC Reuters reddit Twitter

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)

University of Alberta

Academic Calendar Research Services Office Supply Management Services Financial Services Human Resource Services

Journals

Nature Science PLoS Biology PLoS Computational Biology Nucleic Acids Research Bioinformatics

Misc

Stothard Group homepage Stothard Group GitHub repository