New

• Classification toolbox 
  http://stuff.mit.edu/afs/sipb.mit.edu/user/arolfe/matlab/
   
• MATLAB codes for implementation of both OOMP and BOOMP are available
  http://www.ncrg.aston.ac.uk/Projects/BiOrthog
   
• IDEAL (formerly LANS) Pattern Recognition Toolbox
  Kui-yu Chang / LANS Matlab Toolbox
  http://www.lans.ece.utexas.edu/~lans/lans/
   
• Smoothed Data Histogram Toolbox for Matlab / Cluster Visualization with Self-Organizing Maps
  http://www.ofai.at/~elias.pampalk/sdh/ 
   
• Data description toolbox
  http://ida.first.fhg.de/~davidt/dd_tools.html  
   
• The Lazy Learning Toolbox for Use with MATLAB
  Mauro Birattari and Gianluca Bontempi (IRIDIA Universit?Libre de Bruxelles Brussels, Belgium)
  http://iridia0.ulb.ac.be/%7Elazy/lazy.matlab.html
   
• Fast Mobius Transforms
  http://iridia.ulb.ac.be/~psmets/#G
   
• Options Matlab
  http://www.geodise.org/documentation/OptionsMatlab/html/index.htm
   
• Graph Layout Generation Package- This package contains utility functions for drawing small directed or undirected networks (e.g. textbook examples) using Matlab.
  http://staff.science.uva.nl/~cemgil/matlab/layout.html
   
• NLSSOL from Stanford Systems Optimization Laboratory,
  http://tomlab.biz/products/npsol/nlssol.php
   
• http://www-dii.ing.unisi.it/~giorgetti/users.html
   
• Hybrid Toolbox
  Author: Alberto Bemporad
• http://www.dii.unisi.it/hybrid/toolbox/
  The Hybrid Toolbox is a Matlab/Simulink toolbox for modeling and simulating hybrid dynamical systems, for designing and simulating model predictive controllers for linear and for hybrid systems subject to constraints, and for generating equivalent piecewise linear control laws that can be directly embedded as C-code in real-time applications.
  Interfaces used: GLPKMEX, CPLEXMEX, MEXPRESS
   
• Multiparametric Toobox
  By M. Kvasnica, P. Grieder and M. Baotic
  http://control.ee.ethz.ch/~mpt/ 
  The Multi-Parametric Toolbox (MPT) is a free Matlab toolbox for design, analysis and deployment of optimal controllers for constrained linear and hybrid systems. Efficiency of the code is guaranteed by the extensive library of algorithms from the field of computational geometry and multi-parametric optimization. Interfaces used: GLPKMEX, MEXPRESS, CPLEXMEX
   
• YALMIP
  By Johan Lberg
  http://control.ee.ethz.ch/~joloef/yalmip.php 
  YALMIP is a MATLAB toolbox for rapid prototyping of optimization problems. The package initially focused on semi-definite programming, but the latest release extends this scope significantly. YALMIP can now be used for convex linear, quadratic, second order cone and semidefinite programming, as well as for non-convex semi-definite programming, mixed integer, multi-parametric and geometric programming. In addition to this, YALMIP supports a novel feature called automatic dualization which helps the user to derive the (symbolic) dual of general convex cone programs. 
   
• Kernel Density Estimation Toolbox
  http://ssg.mit.edu/~ihler/code/  
   
• Toolbox for complex systems
  http://tocsy.agnld.uni-potsdam.de 
   
• Matlog: Logistics Engineering Matlab Toolbox
  http://www.ie.ncsu.edu/kay/matlog/  
   
• ENTOOL version 1.0
  http://chopin.zet.agh.edu.pl/~wichtel/index.html 
   
• MATLAB Kriging Toolbox 4.0.
  http://www.ai-geostats.org/software/Geostats_software/MATLAB_KRIGING_TOOLBOX.htm 
   
• MATLAB Krigeage Toolbox Introduction for Version 3
  http://globec.whoi.edu/software/kriging/V3/intro_v3.html 
   
• Toolbox which includes the EM algorithm. 
  http://www.spatial-econometrics.com/ 
   
• GEOXP A Matlab Toolbox for Exploratory Spatial Analysis
  http://www.univ-tlse1.fr/GREMAQ/Statistique/geoxppage.htm  
  Doc: http://www.univ-tlse1.fr/GREMAQ/Statistique/geoxppage.htm  
   
• The HFRC toolbox is designed to import, process and manipulate HF Radar data in a relatively easy and consistent way
  http://erizo.ucdavis.edu/~dmk/software/hfrc/hfrc.html  
   
• WFDB library subset for Matlab/Octave
  http://www.physionet.org/physiotools/matlab/wfdb/  
   
• DCPR 
  Jang 
  http://neural.cs.nthu.edu.tw/jang/matlab/toolbox/DCPR/ 
   
• Andreas Wiegmann / Matlab Movies for Windows
  http://familie-wiegmann.de/ALWsMMs/pc.html  
   
• ZSM (zero sum multinomial)
  http://mcgillb.user.msu.edu/zsmcode.html  
   
• Binaural-modeling software for MATLAB/Windows
  http://www.lifesci.sussex.ac.uk/home/Michael_Akeroyd/download2.html 
   
• BOOTSTRAP MATLAB TOOLBOX
  http://www.csp.curtin.edu.au/downloads/bootstrap_toolbox.html  
   
• The DSS package for MATLAB
  DSS Matlab package contains algorithms for performing linear, deflation and symmetric DSS.
  http://www.cis.hut.fi/projects/dss/package/  
   
• Psychtoolbox
  http://www.psychtoolbox.org/download.html 
   
• Multisurface Method Tree with MATLAB
  http://www.cs.wisc.edu/~olvi/uwmp/msmt.html 
   
• A Matlab Toolbox for every single topic !
  http://stommel.tamu.edu/~baum/toolboxes.html 
  eg. BrainStorm - MEG and EEG data visualization and processing
   
• CLAWPACK is a software package designed to compute numerical solutions to hyperbolic partial differential equations using a wave propagation approach
  http://www.amath.washington.edu/~claw/ 
   
• DIPimage - Image Processing Toolbox
   
• PRTools - Pattern Recognition Toolbox (+ Neural Networks) 
   
• NetLab - Neural Network Toolbox
   
• FSTB - Fuzzy Systems Toolbox
   
• Fusetool - Image Fusion Toolbox
  http://www.metapix.de/toolbox.htm 
   
• WAVEKIT - Wavelet Toolbox
   
• Gat - Genetic Algorithm Toolbox 
   
• TSTOOL is a MATLAB software package for nonlinear time series analysis.
  TSTOOL can be used for computing: Time-delay reconstruction, Lyapunov exponents, Fractal dimensions, Mutual information, Surrogate data tests, Nearest neighbor statistics, Return times, Poincare sections, Nonlinear prediction
  http://www.physik3.gwdg.de/tstool/  
   
• MATLAB / Data description toolbox 
  A Matlab toolbox for data description, outlier and novelty detection 
  March 26, 2004 - D.M.J. Tax 
  http://www-ict.ewi.tudelft.nl/~davidt/dd_tools/dd_manual.html 
   
• MBE
  http://www.pmarneffei.hku.hk/mbetoolbox/ 
   
• Betabolic network toolbox for Matlab 
  http://www.molgen.mpg.de/~lieberme/pages/network_matlab.html 
   
• Pharmacokinetics toolbox for Matlab 
  http://page.inf.fu-berlin.de/~lieber/seiten/pbpk_toolbox.html 
   
• The Spider
  The spider is intended to be a complete object orientated environment for machine learning in Matlab. Aside from easy use of base learning algorithms, algorithms can be plugged together and can be compared with, e.g model selection, statistical tests and visual plots. This gives all the power of objects (reusability, plug together, share code) but also all the power of Matlab for machine learning research.
  http://www.kyb.tuebingen.mpg.de/bs/people/spider/index.html 
  
• Schwarz-Christoffel Toolbox
  http://www.mathworks.com/matlabcentral/fileexchange/loadFile.do?objectId=1316&objectType=file# 
   
• XML Toolbox 
   http://www.mathworks.com/matlabcentral/fileexchange/loadFile.do?objectId=4278&objectType=file 
    
• FIR/TDNN Toolbox for MATLAB 
  Beta version of a toolbox for FIR (Finite Impulse Response) and TD (Time Delay) Neural Networks. 
  http://www.cs.utep.edu/interval-comp/dagstuhl.03/oish.pdf 
   

Misc.

•  http://www.dcsc.tudelft.nl/Research/Software/index.html

Astronomy

• Saturn and Titan trajectories ... MALTAB astronomy
  http://sprg.ssl.berkeley.edu/~abrecht/Matlab-codes/  
   

Audio 

• PQevalAudio [options] AFileR AFileT
  http://www.tsp.ece.mcgill.ca/MMSP/Documents/Software/Packages/AFsp/PQevalAudio.html  
   

• TTSBOX: A MATLAB TOOLBOX FOR TEACHING TEXT-TO-SPEECH SYNTHESIS
  http://tcts.fpms.ac.be/publications/papers/2005/ICASSP05_tdmc.pdf
    

• MA Toolbox for Matlab Implementing Similarity Measures for Audio
  http://www.oefai.at/~elias/ma/index.html  
   

• MAD -  Matlab Auditory Demonstrations
  http://www.dcs.shef.ac.uk/~martin/MAD/docs/mad.htm 
   

• Music Analysis - Toolbox for Matlab : Feature Extraction from Raw Audio Signals for Content-Based Music Retrieval
  http://www.ai.univie.ac.at/~elias/ma/  
   

• WarpTB - Matlab Toolbox for Warped DSP
  By Aki H鋜m?and Matti Karjalainen
  http://www.acoustics.hut.fi/software/warp/ 
   

• MATLAB-related Software
  http://www.dpmi.tu-graz.ac.at/~schloegl/matlab/
   

• Biomedical Signal data formats (EEG machine specific file formats with Matlab import routines)
  http://www.dpmi.tu-graz.ac.at/~schloegl/matlab/eeg/
   

• MPEG Encoding library for MATLAB Movies (Created by David Foti)
  It enables MATLAB users to read (MPGREAD) or write (MPGWRITE) MPEG movies. That should help Video Quality project.
   

• Octave by  Christophe COUVREUR (Generates normalized A-weigthing, C-weighting, octave and one-third-octave digital filters)
  http://www.mathworks.com/matlabcentral/fileexchange/loadFile.do?objectType=file&objectId=69 
   

• Source Coding MATLAB Toolbox
  http://www.ece.umn.edu/users/kieffer/programs.html 
   

Bio Medical Informatics (Top)

• NUTMEG: Neurodynamic Utility Toolbox for MEG
  http://tempest.ucsf.edu/~sarang/nutmeg/ 
   

• CGH-Plotter: MATLAB Toolbox for CGH-data Analysis
  Code: http://sigwww.cs.tut.fi/TICSP/CGH-Plotter/ 
  Poster: http://sigwww.cs.tut.fi/TICSP/CSB2003/Posteri_CGH_Plotter.pdf 
   

• The Brain Imaging Software Toolbox
  http://www.bic.mni.mcgill.ca/software/ 
   

• MRI Brain Segmentation
  http://www.mathworks.com/matlabcentral/fileexchange/loadFile.do?objectId=4879 
   

Chemometrics (providing PCA) (Top)

• Matlab Molecular Biology & Evolution Toolbox
  (Toolbox Enables Evolutionary Biologists to Analyze and View DNA and Protein Sequences)
  James J. Cai 
  http://www.pmarneffei.hku.hk/mbetoolbox/ 
   

• Toolbox provided by Prof. Massart research group
  http://minf.vub.ac.be/~fabi/publiek/
   

• Useful collection of routines from Prof age smilde research group
  http://www-its.chem.uva.nl/research/pac
   

• Multivariate Toolbox written by Rune Mathisen
  http://www.bitjungle.com/~mvartools/index.html
   

• Matlab code and datasets
  http://www.acc.umu.se/~tnkjtg/chemometrics/dataset.html 
   

Chaos (Top)

• Chaotic Systems Toolbox 
  http://www.mathworks.com/matlabcentral/fileexchange/loadFile.do?objectId=1597&objectType=file# 
   

• HOSA Toolbox
  http://www.mathworks.nl/matlabcentral/fileexchange/loadFile.do?objectId=3013&objectType=file 
   

Chemistry (Top)

• MetMAP -  (Metabolical Modeling, Analysis and oPtimization alias Met. M. A. P.)
  http://webpages.ull.es/users/sympbst/pag_ing/pag_metmap/index.htm  
   

• DoseLab - A set of software programs for quantitative comparison of measured and computed radiation dose distributions
  http://doselab.sourceforge.net  
   

• GenBank Overview
  http://www.ncbi.nlm.nih.gov/Genbank/GenbankOverview.html 
  Matlab: http://www.mathworks.com/matlabcentral/fileexchange/loadFile.do?objectId=1139  
   

Classification

Control (Top)

• Control Tutorial for Matlab 
  http://www.engin.umich.edu/group/ctm/ 
   

Communications (Top)

• ADSL Toolbox for MATLAB
  http://www.lysator.liu.se/~/backstig/exjobb.html  
   

• Channel Learning Architecture toolbox
  (This Matlab toolbox is a supplement to the article "HiperLearn: A High Performance Learning Architecture")
  http://www.isy.liu.se/cvl/Projects/hiperlearn/ 
   

• Source Coding MATLAB Toolbox
  http://www.ece.umn.edu/users/kieffer/programs.html 
   

• TCP/UDP/IP Toolbox 2.0.4
  http://www.mathworks.com/matlabcentral/fileexchange/loadFile.do?objectId=345&objectType=file  
   

• Home Networking Basis: Transmission Environments and Wired/Wireless Protocols
  Walter Y. Chen
  http://www.mathworks.com/support/books/book5295.jsp?category=new&language=-1 
   
  MATLAB M-files and Simulink models 
  http://www.mathworks.com/matlabcentral/fileexchange/loadFile.do?objectId=3834&objectType=file
   

Engineering (Top)

• WAFO. Wave Analysis for Fatigue and Oceanography 
  http://www.maths.lth.se/matstat/wafo/ 
   

• MatPIV - the Particle Image Velocimetry ( PIV) toolbox for MATLAB
  http://www.math.uio.no/~jks/matpiv/index.html 
   

• OPNML/MATLAB Facilities
  http://www.opnml.unc.edu/OPNML_Matlab/ 
   

• Mesh Generation
  http://www.cs.cornell.edu/home/vavasis/qmg-home.html 
   

• OpenFEM : An Open-Source Finite Element Toolbox 
  http://www.openfem.net/
   

• CALFEM is an interactive computer program for teaching the finite element method (FEM)
  http://www.byggmek.lth.se/Calfem/frinfo.htm  
   

• The Engineering Vibration Toolbox
  http://www.cs.wright.edu/people/faculty/jslater/vtoolbox/vtoolbox.html 
   

• SaGA - Spatial and Geometric Analysis Toolbox
  by Kirill K. Pankratov
  http://puddle.mit.edu/~glenn/kirill/saga.html  
   

• MexCDF and NetCDF Toolbox For Matlab-5&6
  http://woodshole.er.usgs.gov/staffpages/cdenham/public_html/MexCDF/nc4ml5.html
    

• CUEDSID: Cambridge University System Identification Toolbox
  http://www-control.eng.cam.ac.uk/jmm/cuedsid/
   

• Kriging Toolbox
  http://www.ai-geostats.org/software/Geostats_software/MATLAB_KRIGING_TOOLBOX.htm 
   

• Monte Carlo (Dr Nando)
  http://www.cs.ubc.ca/~nando/software.html 
   

• RIOTS - The Most Powerful Optimal Control Problem Solver
  http://blank.hypersurf.com/~adam/RIOTS/ 
   

Data Mining (Top) 

• ARMADA Data Mining Tool version 1.2
  http://www.jamesmalone.plus.com/software.htm   
   

Excel (Top) 

• MATLAB xlsheets
  http://www.mathworks.com/matlabcentral/fileexchange/loadFile.do?objectId=4474&objectType=file 
   
• write2excel 
  http://www.mathworks.com/matlabcentral/fileexchange/loadFile.do?objectId=4414&objectType=file 
   

Finite Element Modeling (FEM) (Top) 

• IFISS Software Package
  Incompressible Flow & Iterative Solver Software Version 2.0
  http://www.ma.umist.ac.uk/djs/software.html 
   

• OpenFEM - An Open-Source Finite Element Toolbox 
  http://www.openfem.net/ 
   

• NLFET - nonlinear finite element toolbox for MATLAB ( framework for setting up, solving, and interpreting results for nonlinear static and dynamic finite element analysis.)
  http://nlfet.sourceforge.net/ 
   

• GetFEM - C++ library for finite element methods elementary computations with a Matlab interface 
  http://www.gmm.insa-tlse.fr/getfem/ 
   

• FELIPE - FEA package to view results ( contains neat interface to MATLAB)
  http://www.brunel.ac.uk/~blstmbr/felipe/
   

Finance (Top)

• A NEW MATLAB-BASED TOOLBOX FOR COMPUTER AIDED DYNAMIC TECHNICAL TRADING
  Stephanos Papadamou and George Stephanides
  Department of Applied Informatics, University Of Macedonia Economic & Social Sciences, Thessaloniki, Greece
  http://www.fenews.com/fen31/one_time_articles/dynamic_tech_trade_matlab6.htm 
  Paper: http://econwpa.wustl.edu:8089/eps/prog/papers/0201/0201001.pdf 
   

• CompEcon Toolbox for Matlab
  http://www4.ncsu.edu/~pfackler/compecon/toolbox.html 
   

Fuzzy

• DENFIS from ECOS Toolbox for Matlab
  http://www.aut.ac.nz/research/research_institutes/kedri/books.htm
   

Genetic Algorithms (Top)

• The Genetic Algorithm Optimization Toolbox (GAOT) for Matlab 5 
  http://www.ie.ncsu.edu/mirage/GAToolBox/gaot/ 
   

• Genetic Algorithm Toolbox
  Written & distributed by Andy Chipperfield (Sheffield University, UK)
  http://www.shef.ac.uk/uni/projects/gaipp/gatbx.html 
  Manual: http://www.shef.ac.uk/~gaipp/ga-toolbox/manual.pdf 
   

• Genetic and Evolutionary Algorithm Toolbox (GEATbx)
  http://www.geatbx.com 
   

• Evolutionary Algorithms for MATLAB
  http://www.geatbx.com/links/ea_matlab.html 
   

• Genetic/Evolutionary Algorithms for MATLAB
  http://www.systemtechnik.tu-ilmenau.de/~pohlheim/EA_Matlab/ea_matlab.html 
   

Graph 

• Graph Analysis Toolbox
  http://eslab.bu.edu/software/graphanalysis/  
  Graph Analysis Toolbox DEMOS 
  http://eslab.bu.edu/software/graphanalysis/graphanalysisDEMOS.html 
   
  The graph analysis toolbox: Image processing on arbitrary graphs
  Leo Grady and Eric L. Schwartz. 
  Technical Report Pending, Boston University, Boston, MA, August 2003. 
  http://eslab.bu.edu/publications/tech-reports/2003/grady2003graph-TR.pdf 
   

Graphics 

• Billiard Simulator for Matlab (Beta Version, 4/12/04).
  Lansel, Steven and Porter, Mason A. [2004].
  Documentation (5/02/04) 
  http://arxiv.org/PS_cache/nlin/pdf/0405/0405003.pdf 
   

• VideoToolbox (C routines for visual psychophysics on Macs by Denis Pelli)
  http://vision.nyu.edu/VideoToolbox/ 
  Paper: http://psych.nyu.edu/pelli/pubs/pelli1997videotoolbox.pdf 
   
• 4D toolbox 
  http://www.nmr.mgh.harvard.edu/~daniel/links/matlab/4DToolbox.html 
   

Images  (Top)

• WHOI Silhouette DIGITIZER Version 1.0 
  http://globec.whoi.edu/software/digi_prog/WHOI_Silhouette_DIGITIZER.htm
   

• Eyelink Toolbox
  http://psychtoolbox.org/eyelinktoolbox/ 
  Paper: http://psychtoolbox.org/eyelinktoolbox/EyelinkToolbox.pdf 
   

• CellStats: Automated statistical analysis of color-stained cell images in Matlab
  http://sigwww.cs.tut.fi/TICSP/CellStats/  
   

• SDC Morphology Toolbox for MATLAB (powerful collection of latest state-of-the-art gray-scale morphological tools that can be applied to image segmentation, non-linear filtering, pattern recognition and image analysis)
  http://www.mmorph.com/ 
   

• Image Acquisition Toolbox
  http://www.mathworks.com/products/imaq/  
   

• Halftoning Toolbox for MATLAB
  http://www.ece.utexas.edu/~bevans/projects/halftoning/toolbox/index.html 
   

• DIPimage - A Scientific Image Processing Toolbox for MATLAB
  http://www.ph.tn.tudelft.nl/DIPlib/dipimage_1.html 
   

• PNM Toolbox
  http://home.online.no/~pjacklam/matlab/software/pnm/index.html 
   

• AngioQuant: quantification of angiogenesis through image analysis 
  http://www.cs.tut.fi/sgn/csb/angioquant/ 
   

ICA / KICA and KPCA  (Top)

• BSS_ORACLE 1.0 has been released!
  http://www.irisa.fr/metiss/bss_oracle/
   

• ICA:DTU Toolbox
  http://mole.imm.dtu.dk/toolbox/menu.html 
   

• MISEP Linear and Nonlinear ICA Toolbox
  http://neural.inesc-id.pt/~lba/ica/mitoolbox.html  
   

• Kernel Independant Component Analysis
  http://www.cs.berkeley.edu/~fbach/kernel-ica/index.htm 
  Matlab: kernel-ica version 1.2 
   

• KPCA- Please check the software section of kernel machines.
   

Kernel  (Top)

• Statistical Pattern Recognition Toolbox 
  http://cmp.felk.cvut.cz/~xfrancv/stprtool/ 
   

• MATLABArsenal A MATLAB Wrapper for Classification 
  http://finalfantasyxi.inf.cs.cmu.edu/tmp/MATLABArsenal.htm  
   

Markov  (Top)

• MapHMMBOX 1.1 - Matlab toolbox for Hidden Markov Modelling using Max. Aposteriori EM
  Prerequisites: Matlab 5.0, Netlab. Last Updated: 18 March 2002.
  http://www.robots.ox.ac.uk/~parg/software/maphmmbox_1_1.tar 
   
• HMMBOX 4.1 - Matlab toolbox for Hidden Markov Modelling using Variational Bayes
  Prerequisites: Matlab 5.0,Netlab. Last Updated: 15 February 2002..
  http://www.robots.ox.ac.uk/~parg/software/hmmbox_3_2.tar  
  http://www.robots.ox.ac.uk/~parg/software/hmmbox_4_1.tar 
   

• Markov Decision Process (MDP) Toolbox for Matlab
  Kevin Murphy, 1999
  http://www.ai.mit.edu/~murphyk/Software/MDP/MDP.zip
   

• Markov Decision Process (MDP) Toolbox v1.0 for MATLAB
  http://www.inra.fr/bia/T/MDPtoolbox/ 
    

• Hidden Markov Model (HMM) Toolbox for Matlab
  http://www.ai.mit.edu/~murphyk/Software/HMM/hmm.html 
   

• Bayes Net Toolbox for Matlab 
  http://www.ai.mit.edu/~murphyk/Software/BNT/bnt.html 
   

Medical (Top)

• Extensible MATLAB Medical image Analysis)
  http://www.bic.mni.mcgill.ca/software/emma/
   

• PWL & PWS Approximation and identification of ODE, Matlab toolbox 
  http://aperest.epfl.ch/docs_repository/software/PWLAppxTbx.zip  
  http://aperest.epfl.ch/docs_repository/software/PWSAppxTbx.zip 
   

• Connectivity matrix identification in heterogeneous networks of oscillators, Matlab toolbox
  Zip: http://aperest.epfl.ch/docs_repository/software/ConnectivityMatrix.zip 
   

• Neuron network identification from spike trains, Matlab toolbox 
  Zip: http://aperest.epfl.ch/docs_repository/software/INCAM.zip 
   

• S synchronization estimator among multivariate time series, Matlab toolbox
  S Toolbox: http://aperest.epfl.ch/docs_repository/software/S_Toolbox.zip  
  DataTest (.zip) and DataTest1 (.zip).
   

• AFNI Matlab Library
  http://afni.nimh.nih.gov/afni/matlab/ 
   
• Group ICA of fMRI Toolbox (GIFT)
  http://icatb.sourceforge.net/ 
   
• EEGLAB Open Source Matlab Toolbox for Physiological Research (formerly ICA/EEG Matlab toolbox)
  http://www.sccn.ucsd.edu/~scott/ica.html 
   

• MATLAB Biomedical Signal Processing Toolbox
  http://bsp.pdx.edu/Toolbox/  
   

• Powerful package for neurophysiological data analysis ( Igor Kagan webpage)
  http://igoresha.virtualave.net/Matlab/Unitret.html  
   

• EEG / MRI Matlab Toolbox
  http://eeg.sourceforge.net/ 
   

• Microarray data analysis toolbox (MDAT): for normalization, adjustment and analysis of gene expression data.
  Knowlton N, Dozmorov IM, Centola M. Department of Arthritis and Immunology, Oklahoma Medical Research Foundation, Oklahoma City, OK, USA 73104. We introduce a novel Matlab toolbox for microarray data analysis. This toolbox uses normalization based upon a normally distributed background and differential gene expression based on 5 statistical measures. The objects in this toolbox are open source and can be implemented to suit your application. AVAILABILITY: MDAT v1.0 is a Matlab toolbox and requires Matlab to run. MDAT is freely available at:
  http://microarray.omrf.org/publications/2004/knowlton/MDAT.zip
   

MIDI  (Top)

• MIDI Toolbox version 1.0 (GNU General Public License)
  http://www.jyu.fi/musica/miditoolbox/ 
   

Misc. (Top)

• Software by Hans Bruun Nielsen 
  http://www2.imm.dtu.dk/~hbn/Software/ 
   

• Using the MATLAB Data AcquisitionToolbox
  Brian D. Storey
  http://icb.olin.edu/fall_02/ec/reading/Card.pdf 
   

• Multiple Precision Toolbox for MATLAB 
  http://www.mathworks.com/matlabcentral/fileexchange/loadFile.do?objectId=6446 
   

• MATLAB-The Graphing Tool
  http://sprg.ssl.berkeley.edu/~abrecht/matlab.html  
   

• 3-D Circuits The Circuit Animation Toolbox for MATLAB
  http://engineering.dartmouth.edu/other/3Dcircuits/
   

• SendMail
  http://carol.wins.uva.nl/~portegie/matlab/sendmail/  
   

• Coolplot
  http://www.reimeika.ca/marco/matlab/coolplots.html 
   

MPI (Matlab Parallel Interface) (Top)

• Cornell Multitask Toolbox for MATLAB
  http://www.tc.cornell.edu/Services/Software/CMTM/ 
   

• Beolab Toolbox for v6.5
  Thomas Abrahamsson (Professor, Chalmers University of Technology, Applied Mechanics, G鰐eborg, Sweden)
  http://www.mathworks.nl/matlabcentral/fileexchange/loadFile.do?objectId=1216&objectType=file  
   

• PARMATLAB
  http://www.mathworks.com/matlabcentral/fileexchange/loadFile.do?objectId=217&objectType=file 
   

Neural Networks  (Top)

• MATLAB Toolbox for Simulation and Visualization of Random Boolean Networks (RBN). Different update modes (synchronous/asynchronous deterministic/non-deterministic), Statistical Functions, Topology Evolution. Complete documentation, function reference, tutorials, gallery and more.
  http://www.activewebs.ch/schwarzer/rbn/index.htm
  http://www.teuscher-research.ch/rbntoolbox/
  Also http://www.mathworks.com/matlabcentral/fileexchange/loadFile.do?objectId=3231&objectType=file
   

• SOM Toolbox 
  http://www.cis.hut.fi/projects/somtoolbox/ 
   

• Bayesian methods for nonlinear classification and regression. (2002)
  Denison, Holmes, Mallick and Smith: Wiley. (Matlab code from the book)
  http://stats.ma.ic.ac.uk/ccholmes/public_html/Book_code/book_code.html
   

• Bayes Net Toolbox for Matlab
  http://www.ai.mit.edu/~murphyk/Software/BNT/bnt.html
    

• NetLab
  http://www.ncrg.aston.ac.uk/netlab/   
   

• Random Neural Networks
  http://www.cs.ucf.edu/~ahossam/rnnsimv2/ 
  ftp: ftp://ftp.mathworks.com/pub/contrib/v5/nnet/rnnsimv2/ 
   

• NNSYSID Toolbox (tools for neural network based identification of nonlinear dynamic systems)
  http://www.iau.dtu.dk/research/control/nnsysid.html 
   

Oceanography  (Top)

• FATHOM - free Matlab toolbox for Multivariate Ecological and Oceanographic Data Analysis
  A collection of functions written by DAVID L. JONES University of Miami - RSMAS.
  Contents: fathom.zip New Features (29-Oct-2003) Draft User's Manual (22-Mar-2003)  
   
• DROG2DDT tracks passive particles in a 2-D flow-field defined on a FEM domain. The integrator is 4th-order Runge-Kutta.
  http://www.opnml.unc.edu/OPNML_Matlab/drog2ddt.m  
   
• WAFO. Wave Analysis for Fatigue and Oceanography
  http://www.maths.lth.se/matstat/wafo/  
   

• ADCP toolbox for MATLAB (USGS, USA)
  Presented at the Hydroacoustics Workshop in Tampa and at ADCP's in Action in San Diego
  http://woodshole.er.usgs.gov/operations/stg/pubs/ADCPtools 
   

• SEA-MAT - Matlab Tools for Oceanographic Analysis
  A collaborative effort to organize and distribute Matlab tools for the Oceanographic Community
  http://sea-mat.whoi.edu/ 
   

• Ocean Toolbox
  http://www.mar.dfo-mpo.gc.ca/science/ocean/epsonde/programming.html
   

• EUGENE D. GALLAGHER
  (Associate Professor, Environmental, Coastal & Ocean Sciences)
  http://www.es.umb.edu/edgwebp.htm
   

Optimization  (Top)

• GP-OLS MATLAB Toolbox
  http://www.fmt.vein.hu/softcomp/gp/
   

• Space Mapping Toolbox
  http://www.imm.dtu.dk/~km/spacemap/spacemap.html 
  Manual: http://www2.imm.dtu.dk/~km/spacemap/manual.pdf 
   
• MODCONS - a MATLAB Toolbox for Multi-Objective Control System Design 
  http://www.eee.kcl.ac.uk/mecheng/jfw/modcons.html 
   

• Lazy Learning Package
  http://iridia.ulb.ac.be/~lazy/ 
   

• SDPT3 version 3.02 -- a MATLAB software for semidefinite-quadratic-linear programming
  http://www.math.nus.edu.sg/~mattohkc/sdpt3.html  
   

• Minimum Enclosing Balls: Matlab Code 
  http://www.compgeom.com/meb/ 
   

• SOSTOOLS Sum of Squares Optimization Toolbox for MATLAB User抯 guide
  http://www.cds.caltech.edu/sostools/sostools.pdf  
   

• PSOt - a Particle Swarm Optimization Toolbox for use with Matlab
  By Brian Birge ... A Particle Swarm Optimization Toolbox (PSOt) for use with the Matlab scientific programming environment has been developed. PSO is
  introduced briefly and then the use of the toolbox is explained with some examples. A link to downloadable code is provided.
   

Plot (Top)

• GrTheory - Graph Theory Toolbox  
  http://www.mathworks.com/matlabcentral/fileexchange/loadFile.do?objectId=4266&objectType=file 
   

• MATLAB basic plot utility
  http://globec.whoi.edu/software/plotting/gbplot/ 
   

Signal Processing  (Top)

• Regularization Tools Version 3.1 (for Matlab Version 6.0)
  http://www2.imm.dtu.dk/~pch/Regutools/regutools.html
   

• Nonlinear Time Series Analysis Component 
  http://www.macalester.edu/~kaplan/Software/Software/mfiles.html 
   

• Filter Design package
  http://www.ee.ryerson.ca:8080/~mzeytin/dfp/index.html 
   

• Deconvolution Toolbox
  http://www.signal.uu.se/Toolbox/DT/  
  Manual: http://www.signal.uu.se/Toolbox/DT/ManualDeconvTool.pdf 
   

• Filter Design with Motorola DSP56K
  http://www.ee.ryerson.ca:8080/~mzeytin/dfp/index.html 
   

• Change Detection and Adaptive Filtering Toolbox
  http://www.sigmoid.se/ 
   

• Signal Processing Toolbox
  http://www.mathworks.com/products/signal/ 
   

• ICA:DTU Toolbox
  http://mole.imm.dtu.dk/toolbox/menu.html 
   

• Time-Frequency Toolbox for Matlab
  http://crttsn.univ-nantes.fr/~auger/tftb.html
   

• VoiceBox - Speech Processing Toolbox
  http://www.ee.ic.ac.uk/hp/staff/dmb/voicebox/voicebox.html 
   

• Least Squared - Support Vector Machines (LS-SVM)
  http://www.esat.kuleuven.ac.be/sista/lssvmlab/ 
   

• WaveLab802 : the Wavelet Toolbox
  By David Donoho, Mark Reynold Duncan, Xiaoming Huo, Ofer Levi
  http://www-stat.stanford.edu/~wavelab/ 
   

• Time-series Matlab scripts
  http://wise-obs.tau.ac.il/~eran/MATLAB/TimeseriesCon.html  
   

• Uvi_Wave Wavelet Toolbox Home Page 
  http://www.gts.tsc.uvigo.es/~wavelets/index.html 
   

• Another

Support Vector Machine (Top)

• SVM and Kernel Methods Matlab Toolbox
  http://asi.insa-rouen.fr/~arakotom/toolbox/index 
   

• MATLAB Support Vector Machine Toolbox
  Dr Gavin Cawley
  School of Information Systems, University of East Anglia
  http://theoval.sys.uea.ac.uk/~gcc/svm/toolbox/  
   

• LS-SVM - SISTA
  http://www.esat.kuleuven.ac.be/sista/lssvmlab/ 
   

• SVM toolboxes
  http://www.cs.wisc.edu/dmi/svm/ 
   

• LSVM Lagrangian Support Vector Machine
  http://www.cs.wisc.edu/dmi/lsvm/ 
   

Statistics  (Top)

• Regularization Tools Version 3.1 (for Matlab Version 6.0)
  http://www2.imm.dtu.dk/~pch/Regutools/index.html 
   

• ENTOOL - Ensemble toolbox for Statistical Learning
  http://zti.if.uj.edu.pl/~merkwirth/entool.htm
   

• Statistical Parametric Mapping (SPM)
  http://www.fil.ion.ucl.ac.uk/spm/ext/ 
   

• Logistic regression 
  http://www.spatial-econometrics.com/ 
   
• SAGA
  http://globec.whoi.edu/software/saga/ 
   
• Multi-Parametric Toolbox (MPT) A tool (not only) for multi-parametric optimization.
  http://control.ee.ethz.ch/~mpt/ 
   
• ARfit: A Matlab package for the estimation of parameters and eigenmodes of multivariate autoregressive models
  http://www.mat.univie.ac.at/~neum/software/arfit/ 
   

• The Dimensional Analysis Toolbox for MATLAB
  Home: http://www.sbrs.de/ 
  Paper: http://www.isd.uni-stuttgart.de/~brueckner/Papers/similarity2002.pdf  
   

• FATHOM for Matlab 
  http://www.rsmas.miami.edu/personal/djones/  
   
• PLS-toolbox
  http://www.eigenvector.com 
   
• Multivariate analysis toolbox (N-way Toolbox - paper)
  http://www.models.kvl.dk/source/nwaytoolbox/index.asp 
   
• Classification Toolbox for Matlab
  http://tiger.technion.ac.il/~eladyt/classification/index.htm  
   
• Matlab toolbox for Robust Calibration
  http://www.wis.kuleuven.ac.be/stat/robust/toolbox.html  
    
• Statistical Parametric Mapping
  http://www.fil.ion.ucl.ac.uk/spm/spm2.html  
   
• EVIM: A Software Package for Extreme Value Analysis in Matlab 
  by Ramazan Gen鏰y, Faruk Selcuk and Abdurrahman Ulugulyagci, 2001.
  Manual (pdf file) evim.pdf - Software (zip file) evim.zip 
   
• Time Series Analysis
  http://www.dpmi.tu-graz.ac.at/~schloegl/matlab/tsa/  
   
• Bayes Net Toolbox for Matlab
  Written by Kevin Murphy
  http://www.ai.mit.edu/~murphyk/Software/BNT/bnt.html 
  Other: http://www.isp.pitt.edu/information/toolboxes.html 
   

• ARfit: A Matlab package for the estimation of parameters and eigenmodes of multivariate autoregressive models
  http://www.gps.caltech.edu/~tapio/arfit/ 
   

• M-Fit
  http://www.ill.fr/tas/matlab/doc/mfit4/mfit.html 
   

• Dimensional Analysis Toolbox for Matlab
  http://www.sbrs.net/
   

• The NaN-toolbox: A statistic-toolbox for Octave and Matlab... handles data with and without MISSING VALUES. 
  http://www-dpmi.tu-graz.ac.at/~schloegl/matlab/NaN/ 
   

• Iterative Methods for Optimization: Matlab Codes
  http://www4.ncsu.edu/~ctk/matlab_darts.html 
   

• Multiscale Shape Analysis (MSA) Matlab Toolbox 2000
  http://www.vision.ime.usp.br/~cesar/projects/multiscale/ 
   

• Multivariate Ecological & Oceanographic Data Analysis (FATHOM)
  From David Jones
  http://www.rsmas.miami.edu/personal/djones/ 
   

• Generalized Linear Models (glmlab)
  http://www.sci.usq.edu.au/staff/dunn/glmlab/glmlab.html 
   

• Spacial and Geometric Analysis (SaGA) toolbox 
  
   

Wavelets (Top)

• MATLAB wavelet coherence package
  http://www.pol.ac.uk/home/research/waveletcoherence/ 
   
• WSPM: Wavelet-based Statistical Parametric Mapping 
  http://bigwww.epfl.ch/demo/wspm/
   
• Biomedical Imaging Group
  http://bigwww.epfl.ch/algorithms.html
   

Web (Top)

• XML Toolbox for Matlab (v3.2.0)
   

(Top)