MATLAB

ADAPTx
[commercial] Automated multivariable system identification and time series analysis software.
http://www.adaptics.com/

Advanced Source Code
Source code for signal processing, image processing, and biometric recognition.
http://www.advancedsourcecode.com

ARfit: Fitting Multivariate Autoregressive Models
Offers functions for estimating parameters of multivariate autoregressive (AR) models, diagnostic checking of fitted models, and analyzing eigenmodes.
http://www.gps.caltech.edu/~tapio/arfit/

ARMASA Toolbox
[free] The power spectrum containing only the significant details is calculated from an estimated time series model. The model order and type are determined automatically, using statistical selection criteria.
http://www.dcsc.tudelft.nl/Research/Software/index.html

Audio Filtering Toolkit
A collection of functions for designing and analyzing industry standard digital audio filters.
http://www.bteaudio.com/software/AudioFilteringToolkit.zip

Bayes Net Toolbox
Software for MATLAB 5.
http://www.cs.ubc.ca/~murphyk/Software/BNT/bnt.html

Biomedical Signal Analysis Software
Software package of various methods for biosignal analysis. Can be adapted for the analysis of time-variant or event-related biosignals.
http://it.uku.fi/biosignal/bssoftware

Blind Watchmaker IFS Applet
Provides an interface for visually evolving a "genotype" vector of floating-point values based on a displayable "phenotype".
http://www.cs.wlu.edu/~levy/bw/

The Bootstrap Toolbox
[free] Functions for resampling, hypothesis testing, and confidence interval estimation.
http://www.csp.curtin.edu.au/downloads/bootstrap_toolbox.html

BrainStorm
A toolbox dedicated to Magnetoencephalography (MEG) and Electroencephalography (EEG) data visualization and processing.
http://neuroimage.usc.edu/brainstorm/

Camera Calibration Toolbox
Utilizes a new bias correction procedure for circular control points and a nonrecursive method for reversing the distortion model.
http://www.ee.oulu.fi/~jth/calibr/

The Cerveau Cafe
User submitted Matlab benchmarks. Lists information comparing different types of hardware with program performance.
http://www.tiger-marmalade.com/~yash/demo/benchmark.html

Chemometrics Toolbox
Provides specialized functions for calibration, including quantitative and qualitative analysis. Includes ordering details.
http://www.chemometrics.com/software/chemometrics.html

COMSOL Norge
Scandinavian distributor of MATLAB, FEMLAB and Maple.
http://www.comsol.no/

Constell, Inc
A toolbox designed for analysis of GPS, GLONASS, and user defined constellations for navigation or communcications.
http://www.constell.org/

Control Tutorials for MATLAB
Covering the analysis and design of automatic control systems.
http://www.engin.umich.edu/group/ctm/

Cornell Multitask Toolbox
Provides a set of development programming tools.
http://www.tc.cornell.edu/Services/Support/Forms/form_cmtm.htm

Cross Recurrence Plot Toolbox
Contains routines for computing recurrence plots and related problems. A command-line application of the programmes is also possible.
http://www.agnld.uni-potsdam.de/~marwan/toolbox

CSIRO matlab/netCDF interface
Used in a to retrieve data from, and information about, existing netCDF files.
http://www.marine.csiro.au/sw/matlab-netcdf.html

Data Visualization Toolbox
Implementing the analytical and graphical methods presented in William S. Cleveland's Visualizing Data.
http://www.datatool.com/prod01.htm

DDE-BIFTOOL
A package for bifurcation analysis of delay differential equations.
http://www.cs.kuleuven.be/cwis/research/twr/research/software/delay/ddebiftool.shtml

Design and Analysis of Computer Experiments
Toolbox for working with kriging approximations to computer models. Includes zip download and reference file in pdf format.
http://www.imm.dtu.dk/~hbn/dace/

Dutchroll Blockset for Simulink
[free] Provides several useful general-purpose Simulink blocks, such as signal generators, gains, switches, and rotation blocks.
http://home.wanadoo.nl/dutchroll/dubsi/dubsi.htm

EasyKrig2.0
The GLOBEC Kriging software package.
http://globec.whoi.edu/software/kriging/easy_krig/easy_krig.html

Easyspec
A small spectrum-analyzer like plotter.
http://www.billauer.co.il/easyspec.html

EIGIFP
Computes a few (algebraiclly) smallest or largest eigenvalues of large symmetric matrices.
http://www.ms.uky.edu/~qye/software.html

EigTool
[free] A GUI (Graphical User Interface) that integrates MATLAB's eigs routine (ARPACK) for finding a few eigenvalues of a large sparse matrix with the (now obsolete) Pseudospectra GUI for computing pseudospectra of matrices.
http://web.comlab.ox.ac.uk/projects/pseudospectra/eigtool/

Engineering Vibration Toolbox
Including single degree of freedom response, response spectrum, finite elements, numerical integration, modal analysis and phase plane analysis.
http://www.cs.wright.edu/people/faculty/jslater/vtoolbox/vtoolbox.html

epsTk
Provides, via a set of .m functions, a toolkit to create powerful encapsulated postscript (.eps) graphs. Most 2D scientific graphics functions are written. The generated .eps-files are very small and can be imported into other documents without loss of quality.
http://www.epstk.de/

Evolutionary Algorithms for MATLAB
A list of available toolboxes for genetic algorithms and genetic programming.
http://www.geatbx.com/links/ea_matlab.html

Factor Analysis Toolbox
The Factor Analysis Toolbox provides a family of specialized MATLAB functions for factor analysis techniques. It is designed to help you learn the principles of target factor analysis and to provide the capabilities necessary for tackling real research and modelling problems.
http://www.chemometrics.com/software/fatb.html

FastICA for MATLAB
Implements the fast fixed-point algorithm for independent component analysis and projection pursuit.
http://www.cis.hut.fi/projects/ica/fastica/

FEMLAB - Multiphysics in MATLAB
[commercial] A powerful interactive environment for modeling and solving scientific and engineering problems involving partial differential equations.
http://www.femlab.com/

Flight Dynamics and Control Toolbox
A Matlab/Simulink toolbox for aircraft dynamics research and flight control system design. Features a detailed flight model, autopilot simulation, and user manual.
http://www.dutchroll.com/

GABLE: A MATLAB Geometric Algebra Tutorial
A tutorial for learning Geometric Algebra, aimed at the sophomore college level.
http://www.cgl.uwaterloo.ca/~smann/GABLE/

Genetic and Evolutionary Algorithm Toolbox
[commercial]
http://www.geatbx.com/

Global Optimization by Multilevel Coordinate Search
MCS is a MATLAB program for bound constrained global optimization using function values only, based on a multilevel coordinate search that balances global and local search.
http://www.mat.univie.ac.at/~neum/software/mcs/

GloptiPoly
A MATLAB/SeDuMi add-on to build and solve convex conic relaxations of non-convex global polynomial optimization problems.
http://www.laas.fr/~henrion/software/gloptipoly/

GPS Signal Simulation Toolbox
[commercial] A set of GPS signal simulation, test, and analysis tools.
http://www.navsys.com/Products/toolbox.htm

Gradient Vector Flow for MATLAB
A variation on active contours, computer-generated curves that move within images to find object boundaries.
http://iacl.ece.jhu.edu/projects/gvf/

The Gravitational Radiation Analysis and Simulation Package
Includes the Gravitational Radiation Toolbox, which provides a MATLAB interface to both GRASP and the Frame Library.
http://www.lsc-group.phys.uwm.edu/~ballen/grasp-distribution/

Growing Cell Structure Visualisation Toolbox
[free] Implements the system described in "Visualisation of biomedical datasets by use of growing cell structure networks: a novel diagnostic classification technique" by Walker AJ, Cross SS, Harrison RF.
http://gcvis.group.shef.ac.uk/

Hidden Markov Model (HMM) Toolbox
Written by Kevin Murphy [free].
http://www.cs.berkeley.edu/~murphyk/Bayes/hmm.html

h2m
Functions for the EM estimation of mixtures and hidden Markov models.
http://www.tsi.enst.fr/~cappe/h2m

Holo
A program which allows the user to visualize the effect of complex maps, especially, but not exclusively, those which are holomorphic.
http://math.rice.edu/~polking/holo.html

HPLOT - Signal Data Visualization and Processing Tool for MATLAB
HPLOT is a dynamic gui tool made for rapid visualization and signal treatment, filtering, FFT and other mathematical operations. By Claudio Gambelli http://www.gambelli.org
http://www.gambelli.org/matlab/hplot/index.html

HUTear Matlab Toolbox version 2.0
A MATLAB toolbox for auditory modeling.
http://www.acoustics.hut.fi/software/HUTear/

ICALAB Toolboxes
ICALAB for Signal Processing and ICALAB for Image Processing are two independent packages for MATLAB that implement a number of efficient algorithms for ICA (independent component analysis).
http://www.bsp.brain.riken.go.jp/ICALAB/

Image Reconstruction Toolbox
M-files for several algorithms for tomographic image reconstruction. Included in collection is a NUFFT MATLAB toolbox that performs fast and accurate nonuniform FFT computations.
http://www.eecs.umich.edu/~fessler/code/

JMatLink
[free] Connects Java and MATLAB. Native methods make it possible to use MATLAB's computational engine inside your own java applications, applets and servlets.
http://www.held-mueller.de/JMatLink/

KFtools for MATLAB
Some simple, fast image processing functions for MATLAB.
http://www.dip.ee.uct.ac.za/~kforbes/KFtools/KFtools.html

Kriging Toolbox
Matlab based toolbox written by Caroline Lafleur and Yves Gratton, INRS-Oceanologie, Universite du Quebec Rimouski.
http://globec.whoi.edu/software/kriging/V3/intro_v3.html

L3NAV Systems
Provider of GPS and Kalman Filtering Toolboxes for MATLAB.
http://www.l3nav.com/

LOBPCG Method
Locally Optimal Block Preconditioned Conjugate Gradient.
http://www-math.cudenver.edu/~aknyazev/software/CG/

MAD - MATLAB Automatic Differentiation
Library of functions and utilities for the automatic differentiation of MATLAB functions and statements. MAD utilizes an optimized class library for the linear combination of derivative vectors.
http://matlabad.com/

MATDS
A MATLAB-based program for dynamical system investigation. Current version allows to compute trajectories, equilibria, Poincare map, Lyapunov exponents and vector field visualization for ordinary differential equation systems.
http://kvm.math.rsu.ru/matds/

Math Forum
Users of the software share tips and advice.
http://mathforum.org/kb/forum.jspa?forumID=80

Mathematical Exploration with MATLAB
By Ke Chen, Peter Giblin and Alan Irving (CUP, 1999). M-files and sample solutions.
http://www.liv.ac.uk/maths/ETC/matbook/

Mathtools.net
MATLAB Portal with links to toolboxes and other resources. Requires Javascript; free registration.
http://www.mathtools.net/MATLAB

MATLAB Automated Testing Tool
Software to generate test matrices, execute simulations of a particular superblock, capture the simulation output, and support analysis of the output.
http://www.cs.umt.edu/RTSL/matt/

MATLAB Depot
A collection of M-files for linear algebra maintained by Michael Tsatsomeros at Washington State University.
http://www.math.wsu.edu/math/faculty/tsat/matlab.html

A Matlab Differentiation Matrix Suite
Provides functions for solving differential equations by the spectral collocation method.
http://dip.sun.ac.za/~weideman/research/differ.html

Matlab Distributed Computation Tutorial
Describes scenarios for monitoring, pipelines and parallel processing. PDF, HTML, source code.
http://www.gaborcselle.com/mdct/

MATLAB FAQ
Frequently asked questions in comp.soft-sys.matlab.
http://www.mit.edu/~pwb/cssm/index.html

MATLAB OPTIMIZATION - TOMLAB
The TOMLAB Optimization Environment is a powerful optimization platform for solving applied optimization problems in MATLAB. TOMLAB provides a wide range of features, tools and services for your solution process.
http://tomopt.com/tomlab/

Matlab Summary and Tutorial
Provided by the University of Florida.
http://www.math.ufl.edu/help/matlab-tutorial/

MatlabTrader
Free tools that use MATLAB to collect stock data, store it in a database, and create an automated trading system.
http://www.MatlabTrader.com

The Matrix Computation Toolbox
[free] A collection of MATLAB M-files containing functions for constructing test matrices, computing matrix factorizations, visualizing matrices, and carrying out direct search optimization.
http://www.maths.man.ac.uk/~higham/mctoolbox/

MatSeis
MatSeis is a seismic toolbox for MATLAB. It provides a time-distance profile plot integrating origin, waveform, travel-time, and arrival data with graphical plot controls, data manipulation, and signal processing functions.
https://www.nemre.nnsa.doe.gov/cgi-bin/prod/nemre/matseis.cgi

Methlab: a MATLAB parody
Site selling merchandise that parodies the MATLAB programming language.
http://www.cafepress.com/matrix_comp

M2HTML
A documentation system for Matlab in HTML.
http://www.artefact.tk/software/matlab/m2html/

Mocha, MATLAB via the WWW
[free] Using MATLAB and a browser together as clients for graphical applications.
http://puddle.mit.edu/~glenn/mocha.html

Modal Control and LFTs
Two toolboxes for use with MATLAB: the Robust Modal Control Toolbox and the Linear Fractional Representation Toolbox.
http://www.cert.fr/fr/dcsd/IDCO/IDCOPUB/perso/Magni/booksandtb.html

MOSEK Optimization Toolbox
Large scale optimization software. Solves linear, quadratic, general convex and mixed integer optimization problems. Includes features list and documentation.
http://www.mosek.com/index.php?id=38

MPEG for MATLAB
MPEG compression algorithms for audio.
http://www.petitcolas.net/fabien/software/mpeg/

Multiflash for MATLAB
[commercial] Provides physical and thermodynamic properties, with multiphase and multicomponent equilibrium calculations, for a wide range of substances.
http://www.khace.com/Products/Multiflash/index.htm

NetCDF Toolbox Home Page
MexCDF and NetCDF Toolbox For Matlab-5
http://mexcdf.sourceforge.net/

Netlab Toolbox
[free] MATLAB software for neural networks and other pattern recognition algorithms. Special features include Bayesian methods, Gaussian Processes and visualisation.
http://www.ncrg.aston.ac.uk/netlab

Numerical Methods with MATLAB
A textbook for third and fourth year undergraduates in engineering and science.
http://www.me.pdx.edu/~gerry/nmm/

ODE Software for MATLAB
Several versions of DFIELD and PPLANE by John C. Polking, available free for use in educational institutions.
http://math.rice.edu/~dfield/

OpenFEM
A finite element toolbox.
http://www.openfem.net/

OPTI-NUM solutions
Reseller of MATLAB, Simulink and related products in Southern Africa. Provides training, technical support, consulting and application development services.
http://www.optinum.co.za/

The Parallel Problems Server
MATLAB 5 front end to the Parallel Problems Server's computational engine. By using MATLAB 5's object oriented programming features, most server operations are completely transparent.
http://www.nersc.gov/~parry/text/ppserver/

Particle Image Velocimetry with Matlab
URAPIV is a free Matlab toolbox for a Particle Image Velocimetry (PIV) analysis.
http://urapiv.tripod.com

PLS_Toolbox
A chemometric toolbox for chemical engineers and analytical chemists to explore their data and build predictive modelsoutines. It is named after the Partial Least Squares (PLS) regression method, the standard calibration method in many chemical applications. (not free)
http://www.eigenvector.com/PLS_Toolbox.html

PNM Toolbox
Read and write PPM (portable pixelmap), PGM (portable graymap), PBM (portable bitmap) and XBM (X11 bitmap) image files. A few other image processing and conversion tools are also included.
http://home.online.no/~pjacklam/matlab/software/pnm/

Podium Technology
Specialises in producing tools for MATLAB/Simulink that enhance their use in generating control systems for embedded control units and their application tools.
http://www.podiumtechnology.co.uk/

Polynomial Toolbox
A package for polynomials, polynomial matrices and their application in systems, signals and control. [commercial]
http://www.polyx.com/

A Practical Introduction to MATLAB
An introduction to some of the most useful features of MATLAB, including plenty of examples.
http://www.math.mtu.edu/~msgocken/intro/intro.html

Probabilistic Model Toolkit
[free] Functions for inference and learning in various static and dynamic probabilistic models such as hidden Markov models, linear dynamic systems, Gaussian mixture models, and factor analyzers.
http://www.hpl.hp.com/downloads/crl/pmt/

Programming in MATLAB
Documentation in text, PS and PDF.
http://xoomer.alice.it/gciabu/engl/matlab/matlab.htm

PROPT - MATLAB Optimal Control Software
A software package intended to solve dynamic optimization problems (ODE and DAE) by code generation for MAD and TOMLAB /SNOPT.
http://tomdyn.com/

PVM Toolbox
Allows PC Linux users with several MATLAB licenses to call the Parallel Virtual Machine library routines from within the MATLAB interpreter.
http://atc.ugr.es/javier-bin/pvmtb_eng

PyMat -- Python to MATLAB Interface
Free download for Unix and Win32 versions.
http://claymore.engineer.gvsu.edu/~steriana/Python/pymat.html

QMG project
The QMG package generates finite element meshes in two and three dimensions. It is free software distributed as C++ source code with MATLAB and Tck/Tk interfaces.
http://www.cs.cornell.edu/home/vavasis/qmg-home.html

ReBEL : Recursive Bayesian Estimation Library
Toolkit of functions and scripts designed to facilitate sequential Bayesian inference (estimation) in general state space models.
http://choosh.csee.ogi.edu/rebel/

Regression Toolbox for Matlab
This Toolbox consists of a collection of m-files for implementing basic multivariate data analysis and regression.
http://www.control.hut.fi/Kurssit/AS-74.191/en.html

Regularized EM algorithm for analysis of incomplete datasets
A regularized expectation-maximization (EM) algorithm for the estimation of mean values and covariance matrices and for the imputation of missing values in large, incomplete datasets.
http://www.gps.caltech.edu/~tapio/imputation/

RIOTS
A MATLAB toolbox for solving optimal control problems.
http://www.accesscom.com/~adam/RIOTS/

The Schwarz-Christoffel Toolbox
Free distribution in ZIP archives.
http://www.math.udel.edu/~driscoll/software/

Scientific/Educational MATLAB Database
Database of educational or scientific MATLAB m-files in Mathematics and Engineering, maintained by the University of Stuttgart, Germany.
http://matlabdb.mathematik.uni-stuttgart.de

SDC Morphology Toolbox for MATLAB
[commercial] Gray-scale morphological tools for image segmentation, non-linear filtering, pattern recognition and image analysis.
http://www.mmorph.com/

SDT FEMLink
Provides bidirectional interfaces with a number of finite element file formats.
http://www.sdtools.com/femlink.html

SEGYMAT
Read and write SEGY data.
http://segymat.sourceforge.net/

Software at MIT: Matlab
Offers documentation, training, and help.
http://web.mit.edu/matlab/www/home.html

Software Techniques Inc.
Modeling, simulation and prototyping of physical, chemical and mechanical systems. Data analysis, graphics and visualization.
http://www.stiwww.com

Solving DDEs with MATLAB
Deals with the solution of delay differential equations with constant delays
http://www.runet.edu/~thompson/webddes/

SOM Toolbox for Matlab
SOM Toolbox is a software library for Matlab 5 (version 5.2 at least) implementing the Self-Organizing Map (SOM) algorithm.
http://www.cis.hut.fi/projects/somtoolbox/

SOSTOOLS
A free sum of squares optimization toolbox for MATLAB.
http://www.aut.ee.ethz.ch/~parrilo/sostools/

Sounds Logical's M-Pack 1
[commercial] A collection of MATLAB functions for processing WAV files of arbitrary size, significantly extending MATLAB's built-in WAV file handling functionality.
http://www.soundslogical.com/products/mpacks/mpack1_intro.html

Sounds Logical's M-Utilities
[commercial] A collection of useful MATLAB "utility" functions including the following: a "winuigetfolder" function, an open browser function, a hard-disk size query function, and a range of window manipulation functions.
http://www.soundslogical.com/products/mpacks/mpacku_intro.html

Spatial Analysis 3D
Freely available MATLAB tools for the analysis and visualisation of 3d point patterns. Includes methods for simulating 3d point patterns.
http://www.nri.ucsb.edu/Labs/breese/SA3D.html

Spatial and Geometric Analysis Toolbox
It doesn't look like this has been updated for a long time. Will only run under MATLAB 4.
http://puddle.mit.edu/~glenn/kirill/saga.html

Spatial Statistics Toolbox
[free] For estimating large-scale spatial autoregressions.
http://www.spatial-statistics.com/

Spectral Methods in MATLAB
Forty short m-files which do everything from demonstrating spectral accuracy on functions of varying smoothness to solving the Poisson, biharmonic, Orr-Sommerfeld, KdV, and Allen-Cahn equations.
http://www.comlab.ox.ac.uk/people/nick.trefethen/spectral.html

Statistical Parametric Mapping
[free] SPM is a software package for MATLAB for the analysis of brain imaging data sequences (fMRI, PET, SPECT, EEG, MEG).
http://www.fil.ion.ucl.ac.uk/spm/

Statistical Pattern Recognition Toolbox
Focuses on the linear discriminant function, including its generalization to quadratic discriminant function by non-linear data mapping, unsupervised learning algorithms and minimax learning algorithms. [free]
http://cmp.felk.cvut.cz/~xfrancv/stprtool/index.html

Structural Dynamics Toolbox
Provides extensions linked to general 3-D finite element modelling, experimental modal analysis and test/analysis correlation.
http://www.sdtools.com/sdt/

A Survey of Parallel MATLAB Projects
Divides projects into 4 approaches to providing parallel functionalities: Communication routines (MPI/PVM); Routines to split up work among multiple sessions; Parallel backend; Compiling into native parallel code.
http://supertech.lcs.mit.edu/~cly/survey.html

System Identification Tool
A collection of M-files implementing several numerical schemes (state estimation, simultaneous state and parameter estimation) within the framework of state space filtering.
http://tocsy.agnld.uni-potsdam.de/sit.php

Technic Solutions
MATLAB and FEMLAB consulting and training based in Tasmania.
http://www.technic.com.au/

Time Frequency Toolbox
Developed for the analysis of non-stationary signals using time-frequency distributions.
http://www-isis.enst.fr/Applications/tftb/iutsn.univ-nantes.fr/auger/tftb.html

Tomlab
[commercial] Provides state-of-the-art optimization, with fast and robust solutions to sparse and dense linear, quadratic and nonlinear programming problems.
http://tomlab.biz/

Tutorial for Control System Toolbox
By Finn Haugen, Telemark College and TechTeach.
http://www.techteach.no/publications/control_toolbox_matlab/cst4.htm

UMFPACK
[free] A set of routines for solving unsymmetric sparse linear systems, Ax=b, using the Unsymmetric MultiFrontal method. Written in ANSI/ISO C, with a MATLAB interface.
http://www.cise.ufl.edu/research/sparse/umfpack/

UNH Math Dept's MATLAB Tutorials
MATLAB Tutorial Information
http://spicerack.sr.unh.edu/~mathadm/tutorial/software/matlab/

WAFO Wave Analysis for Fatigue and Oceanography
[free] A toolbox for statistical analysis and simulation of random waves and random loads.
http://www.maths.lth.se/matstat/wafo

Wavelets and Signal Processing Package for Matlab
[free] WaveLab is a library of MATLAB routines for wavelet analysis, wavelet-packet analysis, cosine-packet analysis and matching pursuit.
http://www-stat.stanford.edu/~wavelab

WaveWarp Audio Toolbox for MATLAB
Modular PC-based real-time audio processing toolkit with seamless integration to the MATLAB environment allowing rapid prototyping of signal processing algorithms at pro-audio sample rates. No peripheral DSP hardware required.
http://www.soundslogical.com/

XTargets
Consulting services and online tutorials for MATLAB, Simulink, and Real-Time Workshop.
http://xtargets.com/

Yahoo Groups: Matlab
Discussion group for users, with a focus on DSP related topics.
http://groups.yahoo.com/group/matlab/