Tools

Tools

This page contains a list of bioinformatics tools/resources and their original web links classified by their function categories. A short description of the approximate function of each tool is provided in its original context. Our scientists have rich experiences in applying these tools/resources to solve bioinformatics problems.

For questions or comments contact us at: ccmb-core@ctools.umich.edu

Analysis package with multiple programs/applications

EMBOSS (http://emboss.sourceforge.net/what/#Uses)

Next-generation sequencing read alignment and assembly programs

ERANGE (http://woldlab.caltech.edu/rnaseq/)

Mosaik + Pyrobayes (http://bioinformatics.bc.edu/marthlab/Software)

Bowtie (http://bowtie-bio.sourceforge.net/index.shtml)

Phred, Phrap, Consed (http://www.phrap.org/phredphrapconsed.html)

Cross_match (http://www.phrap.org/phredphrapconsed.html)

FindPeaks (http://vancouvershortr.sourceforge.net/)

HPeak (http://www.sph.umich.edu/csg/qin/HPeak/)

MACS (http://liulab.dfci.harvard.edu/MACS/)

CISGenome (http://www.biostat.jhsph.edu/~hji/cisgenome/)

SOAP (http://soap.genomics.org.cn)

SHRiMP (http://compbio.cs.toronto.edu/shrimp)

MAQ (http://maq.sourceforge.net/)

Exonerate (http://packages.debian.org/sid/exonerate)

RMAP (http://rulai.cshl.edu/rmap/)

SeqMap (http://biogibbs.stanford.edu/~jiangh/SeqMap/)

ZOOM (http://www.bioinformaticssolutions.com/products/zoom/index.php)

BFAST (https://secure.genome.ucla.edu/index.php/BFAST)

MOM (http://mom.csbc.vcu.edu/)

NovoAlign (http://www.novocraft.com/)

PASS (http://pass.cribi.unipd.it/cgi-bin/pass.pl)

Slider (http://www.bcgsc.ca/platform/bioinfo/software/slider)

BWA (http://maq.sourceforge.net/bwa-man.shtml)

vmatch (http://www.vmatch.de/)

Sequence alignments

Align expressed DNA sequence with a genomic sequence

Sim4 (http://globin.cse.psu.edu/html/docs/sim4.html)

Pairwise alignment

BLASTZ (http://www.bx.psu.edu/miller_lab/)

Bioconductor- Biostrings::pairwiseAlignment) (http://www.bioconductor.org/)

Multiple sequence alignment

ClustalW (http://www.ebi.ac.uk/Tools/clustalw2/index.html)

T-Coffee (http://tcoffee.vital-it.ch/cgi-bin/Tcoffee/tcoffee_cgi/index.cgi?stage1=1&daction=TCOFFEE::Regular&referer0=embnet)

MUSCLE (http://www.drive5.com/muscle/)

Gene set enrichment testing

Genmapp and Mappfinder (http://www.genmapp.org)

DAVID (http://david.abcc.ncifcrf.gov)

Genome browser and comparative analysis

UCSC genome browser (http://genome.ucsc.edu)

Ensembl genome browser (http://www.ensembl.org/index.html)

VISTA genome browser (http://pipeline.lbl.gov/cgi-bin/gateway2)

Argo genome browser (http://www.broad.mit.edu/annotation/argo/)

Ontologies/Standards

HUGO (http://www.hugo-international.org/index.php)

UniProt (http://www.uniprot.org)

GO (http://www.geneontology.org)

CHADO (http://www.gmod.org/wiki/index.php/Schema)

Chebi (http://www.ebi.ac.uk/chebi/)

SBML (http://en.wikipedia.org/wiki/SBML)

MIAME (http://www.mged.org/Workgroups/MIAME/miame.html)

Graph-ML (http://graphml.graphdrawing.org/)

Information retrieval, literature mining and NLP

BioSearch-2D (http://biosearch2d.ncibi.org)

Gene2MeSH (http://gene2mesh.ncibi.org)

Metab2MeSH (http://metab2mesh.ncibi.org)

MiSearch (http://misearch.ncibi.org)

Oncomine (http://www.oncomine.org/)

SAGA (http://saga.ncibi.org)

SciMiner (http://jdrf.neurology.med.umich.edu/SciMiner/)

Protein-protein interactions

Michigan Molecular Interactions (MiMI) (http://mimi.ncibi.org)

MiMI Plugin for Cytoscape (http://mimiplugin.ncibi.org)

HPRD (http://hprd.beta.ibioinformatics.org/)

DIP (http://dip.doe-mbi.ucla.edu/)

BIND (http://bond.unleashedinformatics.com)

MINT (http://mint.bio.uniroma2.it/mint/Welcome.do)

BioGrid (http://www.thebiogrid.org/)

IntAct (http://www.ebi.ac.uk/intact/site/index.jsf)

Pathways analysis

SAGA (http://saga.ncibi.org)

GeneGo© (http://www.genego.com/)

Panther (http://www.pantherdb.org/)

Reactome (http://www.reactome.org/)

Biocarta (http://www.biocarta.com)

KEGG (http://www.genome.jp/kegg/)

GenMapp (http://www.genmapp.org/)

ChiliBot (http://www.chilibot.net)

STKE (http://chemport.ipe.ac.cn/cgi-bin/chemport/getfiler.cgi?ID=pFn4DwA2I8Cni2JeZHAdIQIXlZfQS32c5YEgy0jzdbIlmiDBoPWrP5UcXqwTvOHN&VER=C)

AFCS (http://www.signaling-gateway.org/molecule)

BioCyc (http://www.biocyc.org)

Database search (Similarity & Homology)

NCBI BLAST (http://blast.ncbi.nlm.nih.gov/Blast.cgi)

WU-BLAST (http://www.advbiocomp.com/blast.html)

FASTA and SSEARCH (http://www.ebi.ac.uk/Tools/fasta33/index.html?program=SSEARCH)

MPsrch (http://www.ebi.ac.uk/Tools/MPsrch/index.html)

ScanPS (http://www.ebi.ac.uk/Tools/scanps/index.html)

Transcription factor binding motif search tools

Genomatix© (http://www.genomtix.de)

MEME (http://meme.sdsc.edu/meme4_1/intro.html)

FootPrinter (http://genome.cs.mcgill.ca/cgi-bin/FootPrinter3.0/FootPrinterInput2.pl)

COSMO (http://bio.cs.washington.edu/software.html)

McPromoter (http://tools.igsp.duke.edu/generegulation/McPromoter/)

Molecular data

GeneCards (http://www.genecards.org)

iHOP (http://www.ihop-net.org/UniPub/iHOP)

Protein Atlas (http://www.proteinatlas.org/)

Antibody (http://www.abnova.com.tw/)

Hupo (http://www.hupo.org/research/hai/)

Gene expression and microarray

GEO (http://www.ncbi.nlm.nih.gov/geo/)

ArrayExpress (http://www.ebi.ac.uk/arrayexpress/)

CustomCDF (http://portal.ncibi.org/gateway/tools.php?category=ALL&sortedBy=name&order=ASC&suite=false)

Dapple (http://www.cs.wustl.edu/~jbuhler/dapple/)

Proteomics

CDART (http://www.ncbi.nlm.nih.gov/Structure/lexington/lexington.cgi?cmd=rps)

VAST Search (http://www.ncbi.nlm.nih.gov/Structure/VAST/vastsearch.html)

Cn3D (http://www.ncbi.nlm.nih.gov/Structure/CN3D/cn3d.shtml)

Analysis Tools

NetAffx© (http://www.affymetrix.com/analysis/index.affx)

Illumina© (http://www.illumina.com/)

Ingenuity© (http://www.ingenuity.com)

Bioconductor (http://bioconductor.org/)

SAM (http://www-stat.stanford.edu/~tibs/SAM/)

SignalP (http://www.cbs.dtu.dk/services/SignalP/)

Compute pI/MW (http://www.expasy.ch/tools/pi_tool.html)

Primer3 (http://frodo.wi.mit.edu/cgi-bin/primer3/primer3_www.cgi)

Workflow tools

GenePattern (http://www.broad.mit.edu/cancer/software/genepattern/)

GE Workbench (http://gforge.nci.nih.gov/projects/geworkbench/)

BioMediator (http://www.biomediator.org/)

Visualization tools

Cytoscape (http://www.cytoscape.org)

Omnigraph© (http://www.spasoft.co.uk/omnigraph.html)

SCIRun (http://software.sci.utah.edu/scirun.html)

VTK (TK) (http://www.vtk.org/)

Graphviz, Neato (http://www.graphviz.org)

TouchGraph (http://www.touchgraph.com)

Biolayout (http://www.biolayout.org)

SNP3D (http://www.snps3d.org/)

Treeview (http://taxonomy.zoology.gla.ac.uk/rod/treeview.html)

HyperTree (http://hypergraph.sourceforge.net/hypertree.html)

ToolKits/Programming

BCDE (http://arrayanalysis.mbni.med.umich.edu/draw/)

GenMapp (http://www.genmapp.org)

R (http://www.r-project.org/)

Mathematica© (http://www.wolfram.com/products/mathematica/index.html)

Matlab© (http://www.mathworks.com/products/matlab/)

Biopython, bioruby, bioperl (www.biopython.org , www.bioruby.org , www.bioperl.org)

Others

Reverse complement (http://www.bioinformatics.org/sms/rev_comp.html)