| ToolKits and APIs |
Triplet-SVM |
2005 |
| Workflows |
OMIGA |
2014 |
| ToolKits and APIs |
Piano |
2015 |
| ToolKits and APIs |
LR50 |
2015 |
| Aligners (short read) | SMALT | 2010 |
|---|
| Aligners (short read) | MAQ | 2007 |
|---|
| Assemblers Genomic (long read) | MERACULOUS | 2010 |
|---|
| Assemblers Genomic (short read) | PE-ASSEMBLER | 2010 |
|---|
| Genome Browsers | NCBI MapViewer | 2004 |
|---|
| Multiple Sequence Aligners | PROBCONS | 2005 |
|---|
| Multiple Sequence Aligners | MAFFT | 2002 |
|---|
| Sequence Tools | Strelka | 2012 |
|---|
| Sequence Tools | CD-HIT | 2006 |
|---|
| Structure Modelling | PSIPRED | 1999 |
|---|
| Structure Visualisation | Jmol | 2001 |
|---|
| ToolKits and APIs | AMPLICONNOISE | 2010 |
|---|
| ToolKits and APIs | PLINK | 2007 |
|---|
| ToolKits and APIs | UTGB | 2007 |
|---|
| ToolKits and APIs | LAGAN | 2003 |
|---|
| Workflows | TAVERNA | 2003 |
|---|
| Workflows | eHIVE | 2000 |
|---|
| Aligners (pairwise) | JALIGNER | 2010 |
|---|
| Aligners (pairwise) | ZOOM | 2008 |
|---|
| Aligners (pairwise) | EXONERATE | 2005 |
|---|
| Aligners (pairwise) | ACT | 2005 |
|---|
| Aligners (pairwise) | SSAHA | 2003 |
|---|
| Aligners (pairwise) | BLAT | 2002 |
|---|
| Aligners (pairwise) | SSAHA2 | 2001 |
|---|
| Aligners (pairwise) | VMATCH | 2000 |
|---|
| Aligners (pairwise) | MASKERAID | 2000 |
|---|
| Aligners (pairwise) | MUMmer | 1999 |
|---|
| Aligners (pairwise) | HMMER | 1998 |
|---|
| Aligners (pairwise) | CROSSMATCH | 1992 |
|---|
| Aligners (pairwise) | BLAST NCBI | 1990 |
|---|
| Aligners (pairwise) | FASTA | 1988 |
|---|
| Aligners (short read) | CASAVA | XX |
|---|
| Aligners (short read) | rna-star | 2012 |
|---|
| Aligners (short read) | GMAP/GSNAP | 2011 |
|---|
| Aligners (short read) | BWA | 2009 |
|---|
| Aligners (short read) | BFAST | 2009 |
|---|
| Aligners (short read) | NOVOALIGN | 2009 |
|---|
| Aligners (short read) | SOAP | 2008 |
|---|
| Aligners (short read) | Bowtie | 2008 |
|---|
| Assemblers (mRNA) | Trinity | 2011 |
|---|
| Assemblers (mRNA) | OASES | 2010 |
|---|
| Assemblers (mRNA) | CUFFLINKS | 2009 |
|---|
| Assemblers (mRNA) | UNIGENE | 2003 |
|---|
| Assemblers Genomic (long read) | PRICE | 2011 |
|---|
| Assemblers Genomic (long read) | QUAKE | 2010 |
|---|
| Assemblers Genomic (long read) | FORGE | 2009 |
|---|
| Assemblers Genomic (long read) | OLIGOZIP | 2007 |
|---|
| Assemblers Genomic (long read) | NEWBLER | 2005 |
|---|
| Assemblers Genomic (long read) | SEQCLEAN | 2004 |
|---|
| Assemblers Genomic (long read) | PHUSION(2) | 2003 |
|---|
| Assemblers Genomic (long read) | ARACHNE | 2002 |
|---|
| Assemblers Genomic (long read) | PCAP | 2001 |
|---|
| Assemblers Genomic (long read) | MIRA 97 | 1997 |
|---|
| Assemblers Genomic (long read) | CELERA | 1997 |
|---|
| Assemblers Genomic (short read) | SPADES | 2012 |
|---|
| Assemblers Genomic (short read) | SOAP: DE NOVO 2 | 2009 |
|---|
| Assemblers Genomic (short read) | SGA | 2009 |
|---|
| Assemblers Genomic (short read) | BAMBUS 2 09 | 2009 |
|---|
| Assemblers Genomic (short read) | CONTRAIL | 2009 |
|---|
| Assemblers Genomic (short read) | ABYSS | 2009 |
|---|
| Assemblers Genomic (short read) | CORTEX_CON_RP | 2008 |
|---|
| Assemblers Genomic (short read) | ALLPATHS-LG | 2007 |
|---|
| Assemblers Genomic (short read) | VELVET | 2007 |
|---|
| Database/Warehouse | MISO | 2012 |
|---|
| Database/Warehouse | ENA | 2012 |
|---|
| Database/Warehouse | PFAM | 2011 |
|---|
| Database/Warehouse | CHADO | 2010 |
|---|
| Database/Warehouse | CHEBI | 2010 |
|---|
| Database/Warehouse | TRANSMART | 2009 |
|---|
| Database/Warehouse | CHEMBL | 2008 |
|---|
| Database/Warehouse | INTERMINE | 2007 |
|---|
| Database/Warehouse | BIOWAREHOUSE | 2006 |
|---|
| Database/Warehouse | INTERPRO | 2005 |
|---|
| Database/Warehouse | bioMART | 2003 |
|---|
| Database/Warehouse | UNIPROT | 2003 |
|---|
| Database/Warehouse | bioSQL | 2001 |
|---|
| Database/Warehouse | CATH | 1997 |
|---|
| Database/Warehouse | PROSITE | 1989 |
|---|
| Database/Warehouse | GENBANK | 1982 |
|---|
| Database/Warehouse | PDB | 1971 |
|---|
| Gene Prediction (mRNA) | SNAP | 2011 |
|---|
| Gene Prediction (mRNA) | MAKER | 2011 |
|---|
| Gene Prediction (mRNA) | AUGUSTUS | 2009 |
|---|
| Gene Prediction (mRNA) | MGENE | 2008 |
|---|
| Gene Prediction (mRNA) | JIGSAW | 2005 |
|---|
| Gene Prediction (mRNA) | ENSEMBL PIPELINE
| 2000 |
|---|
| Gene Prediction (mRNA) | EUGENE | 1999 |
|---|
| Gene Prediction (mRNA) | FGENESH | 1999 |
|---|
| Gene Prediction (mRNA) | GLIMMER 3 | 1998 |
|---|
| Gene Prediction (mRNA) | GENSCAN | 1997 |
|---|
| Gene Prediction (ncRNA) | RNAfold | 2010 |
|---|
| Gene Prediction (ncRNA) | MIRDEEP | 2008 |
|---|
| Gene Prediction (ncRNA) | tRNAscan | 1997 |
|---|
| Genome Browsers | TRIPOD | XX |
|---|
| Genome Browsers | DALLIANCE BROWSER | 2010 |
|---|
| Genome Browsers | SAVANT | 2010 |
|---|
| Genome Browsers | IGV | 2008 |
|---|
| Genome Browsers | ARGO | 2007 |
|---|
| Genome Browsers | JBROWSE | 2007 |
|---|
| Genome Browsers | SEQMONK | 2007 |
|---|
| Genome Browsers | IGB | 2004 |
|---|
| Genome Browsers | APOLLO | 2002 |
|---|
| Genome Browsers | GBROWSE | 2002 |
|---|
| Genome Browsers | ARTEMIS | 2002 |
|---|
| Genome Browsers | UCSC | 2001 |
|---|
| Genome Browsers | ENSEMBL BROWSER | 2000 |
|---|
| Multiple Sequence Aligners | PROT PAL | 2012 |
|---|
| Multiple Sequence Aligners | PRANK | 2010 |
|---|
| Multiple Sequence Aligners | FSA | 2008 |
|---|
| Multiple Sequence Aligners | PECAN | 2006 |
|---|
| Multiple Sequence Aligners | MAVID | 2004 |
|---|
| Multiple Sequence Aligners | MUSCLE | 2004 |
|---|
| Multiple Sequence Aligners | T-COFFEE | 2000 |
|---|
| Multiple Sequence Aligners | CLUSTALW | 1994 |
|---|
| Other Aligners | Bismark | 2010 |
|---|
| Other Aligners | Mauve | 2010 |
|---|
| Other Aligners | DALI | 2003 |
|---|
| Sequence Tools | MUTECT | 2013 |
|---|
| Sequence Tools | RSEM | 2012 |
|---|
| Sequence Tools | FLEXBAR | 2012 |
|---|
| Sequence Tools | VARIANTTOOLS | 2011 |
|---|
| Sequence Tools | RNNOTATOR | 2011 |
|---|
| Sequence Tools | ANNOVAR | 2011 |
|---|
| Sequence Tools | FastQC | 2010 |
|---|
| Sequence Tools | DENDROPY | 2010 |
|---|
| Sequence Tools | GENEPOOL | 2010 |
|---|
| Sequence Tools | FASTX-Toolkit | 2009 |
|---|
| Sequence Tools | METABIOME | 2009 |
|---|
| Sequence Tools | TOPHAT | 2008 |
|---|
| Sequence Tools | GENEDATA | 2008 |
|---|
| Sequence Tools | NESTEDMICA | 2005 |
|---|
| Sequence Tools | JALVIEW | 2004 |
|---|
| Sequence Tools | MEME | 2003 |
|---|
| Sequence Tools | INTEGROMICS | 2003 |
|---|
| Sequence Tools | MATCH | 2003 |
|---|
| Sequence Tools | MASCOT | 1999 |
|---|
| Sequence Tools | SRS | 1997 |
|---|
| Sequence Tools | REPEATMASKER | 1996 |
|---|
| Structure Modelling | TARGETP | 2007 |
|---|
| Structure Modelling | Hhpred | 2005 |
|---|
| Structure Modelling | SWISS-MODEL | 2003 |
|---|
| Structure Modelling | MODELLER | 2003 |
|---|
| Structure Modelling | TMHMM | 1998 |
|---|
| Structure Modelling | SIGNALP | 1997 |
|---|
| Structure Modelling | ROSETTA | 1996 |
|---|
| Structure Modelling | THREADER | 1992 |
|---|
| Structure Visualisation | PYMOL | XX |
|---|
| Structure Visualisation | CHIMERA | 2004 |
|---|
| Structure Visualisation | RasMol | 1995 |
|---|
| ToolKits and APIs | MRBAYES | XX |
|---|
| ToolKits and APIs | PARTEK | XX |
|---|
| ToolKits and APIs | GENESPRING | XX |
|---|
| ToolKits and APIs | GENABEL | 2012 |
|---|
| ToolKits and APIs | SRNA WORKBENCH UEA | 2011 |
|---|
| ToolKits and APIs | AVADIS NGS | 2010 |
|---|
| ToolKits and APIs | SAMtools | 2009 |
|---|
| ToolKits and APIs | QIIME | 2009 |
|---|
| ToolKits and APIs | Picard | 2009 |
|---|
| ToolKits and APIs | VCFtools | 2009 |
|---|
| ToolKits and APIs | GATK | 2009 |
|---|
| ToolKits and APIs | DNANEXUS | 2009 |
|---|
| ToolKits and APIs | UGENE | 2008 |
|---|
| ToolKits and APIs | PATHWAY TOOLS | 2008 |
|---|
| ToolKits and APIs | APSAMPLER | 2005 |
|---|
| ToolKits and APIs | GENEIOUS | 2005 |
|---|
| ToolKits and APIs | CLC BIO | 2005 |
|---|
| ToolKits and APIs | PHASTCONS | 2004 |
|---|
| ToolKits and APIs | BioPython | 2003 |
|---|
| ToolKits and APIs | BIOCONDUCTOR | 2001 |
|---|
| ToolKits and APIs | EMBOSS | 2000 |
|---|
| ToolKits and APIs | BIOJAVA | 2000 |
|---|
| ToolKits and APIs | ENSEMBL API | 2000 |
|---|
| ToolKits and APIs | bioRUBY | 2000 |
|---|
| ToolKits and APIs | bioPERL | 2000 |
|---|
| ToolKits and APIs | PAML | 1997 |
|---|
| ToolKits and APIs | PHYLIP | 1981 |
|---|
| Workflows | GENEXPLAIN | 2010 |
|---|
| Workflows | KNIME | 2008 |
|---|
| Workflows | GALAXY | 2007 |
|---|
| Workflows | PIPELINE PILOT | 1999 |
|---|
