Bioinformatics software

 

This list includes all types of software as known for microarray, protein modeling, promoter recognition and sequence analysis. Further, they could be available publicly or commercially. Some offer source code and some do not. In case the link do not point to the software, it must be linking to a page that has listing of a number of software

Sl. No. Name of software/ collection Category Author & Organization Available at, and Terms & conditions
1 cDNA Microarray Analysis software MA Wong Lab, Department of Biostatistics, Harvard School of Public Health Cite the main reference paper if results obtained from this software are used in manuscripts:
George C. Tseng, Min-Kyu Oh, Lars Rohlin, James C. Liao, Wing Hung Wong (2001) Issues in cDNA microarray analysis: quality filtering, channel normalization, models of variations and assessment of gene effects, Nucleic Acids Res v29
2 GeneX SA NCGR  
3 Gene Cluster ANN Lander & Golub, Whitehead Institute MIT Available from the authors; email at [email protected] or [email protected]
4 Tree View MA Micheal Eisen, Lawrence Berkeley National Laboratory runs on DOS, Windows, rana.lbl.gov/EisenSoftware.htm
5 J-Express MA Bjarte Dysvik & Inge Jonassen, University of Bergen  
6 X Cluster ANN Sherlock, Stanford University runs on MS-DOS, Unix; Software offers the self-organizing feature map clustering and k-means clustering, is available at genome-www.stanford.edu/ ~sherlock/tutorial.html
7 SOTA ANN   runs on DOS, Windows, http://www.cnb.uam.es/~bioinfo/Software/sota/sotadocument.html
8 Kimono MA    
9 Xdigitise MA    
10 F-Scan MA    
11 ScanAlze MA   rana.lbl.gov/EisenSoftware.htm
12 Cluster ANN Micheal Eisen

Lawrence Berkeley National Laboratory

 rana.lbl.gov/EisenSoftware.htm
13 GMEP ANN   runs on Unix, Combined expression data and sequence analysis software available at rana.lbl.gov/EisenSoftware.htm
14 GeneXplorer Vis Sherlock, Stanford University runs on Unix, Web based gene clustering interface available at genome-www.stanford.edu/ ~sherlock/tutorial.html
15 SOMViewer ANN Sherlock, Stanford University runs on Windows, Self-organizing map viewer software available at genome-www.stanford.edu/ ~sherlock/tutorial.html
16 Extended SOM ANN   runs on DOS
17 xsom and wsom ANN   runs on DOS, Windows
18 WebSOM ANN   runs on Windows
19 SVM ANN   runs on DOS
20 lSVM ANN   runs on DOS
21 GlimmerM GFA The Institute of Genomic Research (TIGR) www.tigr.org/software
22 Glimmer GFA TIGR www.tigr.org/software
23 GeneSplicer GFA TIGR www.tigr.org/software
24 TransTerm GFA TIGR www.tigr.org/software
25 RepeatFinder GFA TIGR www.tigr.org/software
26 RBSFinder GFA TIGR www.tigr.org/software
27 Combiner GFA TIGR Compatible with GlimmerM, Genscan, Fgenes, GRAIL, GeneMark.HMM www.tigr.org/software
28 Autoseq tools GFA TIGR www.tigr.org/software
29 Hexamer Based Quality Control Method (hbqcm) GFA TIGR www.tigr.org/software
30 MUMmer 2 SA TIGR High performance SA, www.tigr.org/software
31 AAT Package SA TIGR www.tigr.org/software
32 btab SA TIGR www.tigr.org/software
33 grasta SA TIGR runs on Solaris, www.tigr.org/software
34 BAMBUS SA TIGR runs on Linux, www.tigr.org/software
35 Assembler SA TIGR www.tigr.org/software
36 Lucy MA TIGR runs on Windows; available at www.tigr.org/software
37 MIDAS MA TIGR runs on JDK 1.3; available at www.tigr.org/software
38 MADAM MA TIGR runs on JDK 1.3.1; available at www.tigr.org/software
39 Multi Experiment Viewer (MEV) MA TIGR runs on JRE 1.2 and J3D 1.2, available at www.tigr.org/software
40 Array Viewer MA TIGR runs on Java, available at www.tigr.org/software
41 Spotfinder MA TIGR runs on C/C++ for Windows NT/98; available at www.tigr.org/software
42 McCoder MA TIGR runs on Windows 9x/2000/NT, available at www.tigr.org/software
43 Genscan SA    
44 GRAIL II SA    
45 GeneMark.HMM SA    
46 Fgenes SA    
47 GeneScan SA Ramakrishna Ramaswamy, Jawaharlal Nehru University Available on request from [email protected]
48 GeneParser 2 SA    
49 GenLang SA    
50 SORFIND SA    
51 Dragon Promoter Finder (DPF) version 1.2 PR V B Bajic, et al, Laboratories for IT, Singapore http://sdmc.krdl.org.sg/promoter
52 Promoter 2.0 PR S Knudsen www.cbs.dtu.dk/services/Promoter
53 Promoter Inspector PR   http://www.genomatix.de/
54 Neural Network Promoter Prediction (NNPP) ver 2.1 PR M G Reese and et al www.fruitfly.org/seq_tools/promoter.html
55 LabelSOM ANN A Rauber, D Merkl www.ifs.tuwien.ac.at/~andi
56 Growing Hierarchical SOM (GHSOM) ANN A Rauber, M Dittenbach, D Merkl www.ifs.tuwien.ac.at/~mbach

www.ifs.tuwien.ac.at/~andi

57 EPCLUST ANN Jaak Vilo, European Bioinformatics Institute ep.ebi.ac.uk/EP/EPCLUST/
58 Exact String matching algorithms in Java DM Christian Charras

Tierry Lecroq

 www-igm.univ-mlv.fr/~lecroq/string
59 PERL PL   republic.perl.com
60 The LEDA library DM   Library of efficient datatypes and algorithms available at www.mpi-sb.mpg.e/LEDA/leda.html
61 Information retrieval projects DM   www.cs.jhu.edu/~weiss/projects.html
62 The Stony Brook Algorithm Repository DM   www.cs.sunysb.edu/~algorithm
63 GLIMPSE and AGREP DM Arizona University A tool to search entire file system available at glimpse.cs.arizona.edu
64 HARVEST DM   Information discovery and access system available at harvest.transarc.com
65 AGREP DM   runs on DOS, OS/2, Windows 95/NT, www.tgries.de/agrep
66 Handbook of Algorithms and Data Structures DM University of Chile source code available at www.dcc.uchile.cl/~rbaeza/handbook/hbook.html
67 Information retrieval data structures & algorithms DM University of Chile source code available at www.dcc.uchile.cl/~rbaeza/irbook/irbook.html
68 FIRE & SPARE DM   C++ implementation of algorithms for finite automata, transducers, pattern matching of keywords and regular expressions, at http://www.openfire.org/
69 Listing of programming resources on web DM University of Montreal www2.iro.umontreal.ca/~ratib/code
70 Algorithms archive DM Florian Schintke, Berlin user.cs.tu-berlin.de/~schintke/algorithms/indexe.html
71 Library of Computational Biology Programs DM   csweb.haifa.ac.il/library
72 ELAN DM   A language where (equational) pattern matching plays a fundamental role, at elan.loria.fr
73 Tree structures for algorithmic problems on strings DM Glasgow University suffix trees, suffix arrays software, at www.dcs.gla.ac.uk/research/algorithms/sbst
74 Suffix trees applets DM Moritz G Maaß www.informatik.tu-muenchen.de/~maass/suffix.html
75 Suffix trees applets DM Craig Nevill-Manning, Rutgers University sequence.rutgers.edu/st
76 Compact Affix Trees applet DM Moritz G Maaß www.informatik.tu-muenchen.de/~maass/at
77 SAM SA   sequence alignment and modeling, at www.cse.ucsc.edu/research/compbio/sam.html
78 Isearch DM   software for indexing and searching text documents, at www.etymon.com/search
79 LPM and PAISLEI IDE DM Laleh Laleh's pattern matcher system for Win 32 systems qtj.n3.net/~lpm
80 Icon programming language PL Arizona University homepage at www.cs.arizona.edu/icon
81 SNOBOL4 and SPITBOL programming languages PL   http://www.snobol4.com/
82 strmat package DM   exact string matching and suffix trees, at www.cs.ucdavis.edu/~gusfield/strmat.html
83 XPARAL DM   graphical computation of parameterized alignments, at theory.cs.ucdavis.edu/~stevensk
84 GPL: Graph template library DM   www.fmi.uni-passau.e/Graphlet/GTL
85 SMAA: String matching algorithm animation DM   www.dcc.ufmg.br/~cassia/smaa/english
86 nrgrep DM University of Chile fast and flexible pattern matchine, at www.dcc.uchile.cl/~gnavarro/pubcode
87 Algorithm archive DM Scott Gasch wannabe.guru.org/alg
88 Boyer-Moore applet DM Dieter Bühler sunburn.informatik.uni-tuebingen.de/~buehler/BM/BM.html
89 Aho-Corasick applet DM Dieter Bühler sunburn.informatik.uni-tuebingen.de/~buehler/AC/AC.html
90 Naive, KMP and BM pattern matching algorithms applet DM Masayuki Takeda www.i.kyushu-u.ac.jp/~takeda/PM_DEMO/e.html
91 Multi DM Stefan Edelkamp Efficient multi-suffix tree string dictionary, at www.informatik.uni-freiburg.de/~edelkamp/MultiSuffixTree
92 grappe DM Kucherov pattern matching with wildcards, at www.loria.fr/~kucherov/SOFTWARE/grappe-3.0/grappe-3.0-en.html
93 Bioperl PL   http://www.bioperl.org/
94 MGED MA Microarray Gene Expression Data (MGED) Society http://www.mged.org/
95 BLAT SA   High-performance SA www.soe.ucsc.edu/~kent
96 FLAG SA ITRI High-performance SA flag.itri.org.tw
97 MPSRCH SA   High-performance SA http://www.anedabio.com/
98 BioSpice PP   www.lbl.gov/~aparkin
99 PatternHunter SA   High-performance SA http://www.bioinformaticssolutions.com/
100 WABA SA   High-performance SA www.soe.ucsc.edu/~kent
101 BioQuest PP   omega.cc.umb.edu/~bwhite/ek.html
102 DBSolve PP   websites.ntl.com/~igor.goryanin
103 DynaFit PP   http://www.biokin.com/
104 E-Cell PP   http://www.e-cell.org/
105 Electronic Arc PP   home.xnet.com/~selkovjr/ElectricArc
106 Gepasi PP   http://www.gepasi.org/
107 Jarnac/ JDesigner PP Caltech www.cds.caltech.edu/~hsauro
108 NetBuilder PP   strc.herts.ac.uk/bio/maria/NetBuilder
109 StochSim PP Cambridge University www.zoo.cam.ac.uk/comp-cell/StochSim.html
110 VCell PP   http://www.nrcam.uchc.edu/
111 WinScamp PP Caltech www.cds.caltech/edu/~hsauro
112 DigitalCell/ VisualCell PP   http://www.gnsbiotech.com/
113 PathwayPrism PP   http://www.physiome.com/
114 PhysioLab PP   http://www.entelos.com/
115 CellML PL   Cell markup language, http://www.cellml.org/
116 SBML PL   Systems Biology Markup Language, http://z/D:/tvpweb/online.htmwww.cds.caltech.edu/erato/sbml/docs
117 BioPathways Consortium     http://www.biopathways.org/
118        

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